diff --git a/CHANGELOG.next.asciidoc b/CHANGELOG.next.asciidoc
index 2eaf3d282e23..fcced9f93ad2 100644
--- a/CHANGELOG.next.asciidoc
+++ b/CHANGELOG.next.asciidoc
@@ -311,6 +311,7 @@ https://github.com/elastic/beats/compare/v7.0.0-alpha2...master[Check the HEAD d
 - Add module for ingesting Cisco FTD logs over syslog. {pull}13286[13286]
 - Update CoreDNS module to populate ECS DNS fields. {issue}13320[13320] {pull}13505[13505]
 - Parse query steps in PostgreSQL slowlogs. {issue}13496[13496] {pull}13701[13701]
+- Add support to set the document id in the json reader. {pull}5844[5844]
 
 *Heartbeat*
 
diff --git a/filebeat/docs/inputs/input-common-harvester-options.asciidoc b/filebeat/docs/inputs/input-common-harvester-options.asciidoc
index 8f161006416e..c7f053dfdc01 100644
--- a/filebeat/docs/inputs/input-common-harvester-options.asciidoc
+++ b/filebeat/docs/inputs/input-common-harvester-options.asciidoc
@@ -191,6 +191,10 @@ must be at the top level in the JSON object and the value associated with the
 key must be a string, otherwise no filtering or multiline aggregation will
 occur.
 
+*`document_id`*:: Option configuration setting that specifies the JSON key to
+set the document id. If configured, the field will be removed from the original
+json document and stored in `@metadata.id`
+
 *`ignore_decoding_error`*:: An optional configuration setting that specifies if
 JSON decoding errors should be logged or not. If set to true, errors will not
 be logged. The default is false.
diff --git a/filebeat/input/log/harvester.go b/filebeat/input/log/harvester.go
index 8abe9fcf559c..fd5c8c8dd6d0 100644
--- a/filebeat/input/log/harvester.go
+++ b/filebeat/input/log/harvester.go
@@ -360,15 +360,21 @@ func (h *Harvester) onMessage(
 		jsonFields = f.(common.MapStr)
 	}
 
+	var meta common.MapStr
 	timestamp := message.Ts
-
 	if h.config.JSON != nil && len(jsonFields) > 0 {
-		ts := readjson.MergeJSONFields(fields, jsonFields, &text, *h.config.JSON)
+		id, ts := readjson.MergeJSONFields(fields, jsonFields, &text, *h.config.JSON)
 		if !ts.IsZero() {
 			// there was a `@timestamp` key in the event, so overwrite
 			// the resulting timestamp
 			timestamp = ts
 		}
+
+		if id != "" {
+			meta = common.MapStr{
+				"id": id,
+			}
+		}
 	} else if &text != nil {
 		if fields == nil {
 			fields = common.MapStr{}
@@ -379,6 +385,7 @@ func (h *Harvester) onMessage(
 	err := forwarder.Send(beat.Event{
 		Timestamp: timestamp,
 		Fields:    fields,
+		Meta:      meta,
 		Private:   state,
 	})
 	return err == nil
diff --git a/filebeat/tests/files/logs/json_id.log b/filebeat/tests/files/logs/json_id.log
new file mode 100644
index 000000000000..283db704b1dd
--- /dev/null
+++ b/filebeat/tests/files/logs/json_id.log
@@ -0,0 +1,3 @@
+{"timestamp":"2016-04-05T18:47:18.444Z","level":"INFO","logger":"iapi.logger","thread":"JobCourier4","appInfo":{"appname":"SessionManager","appid":"Pooler","host":"demohost.mydomain.com","ip":"192.168.128.113","pid":13982},"userFields":{"ApplicationId":"PROFAPP_001","RequestTrackingId":"RetrieveTBProfileToken-6066477"},"source":"DataAccess\/FetchActiveSessionToken.process","msg":"FetchActiveSessionToken process ended", "type": "test", "id": "0"}
+{"timestamp":"2016-04-05T18:47:18.444Z","level":"INFO","logger":"iapi.logger","thread":"JobCourier4","appInfo":{"appname":"SessionManager","appid":"Pooler","host":"demohost.mydomain.com","ip":"192.168.128.113","pid":13982},"userFields":{"ApplicationId":"PROFAPP_001","RequestTrackingId":"RetrieveTBProfileToken-6066477"},"source":"DataAccess\/FetchActiveSessionToken.process","msg":"FetchActiveSessionToken process ended", "type": 5, "id": "1"}
+{"timestamp":"2016-04-05T18:47:18.444Z","level":"INFO","logger":"iapi.logger","thread":"JobCourier4","appInfo":{"appname":"SessionManager","appid":"Pooler","host":"demohost.mydomain.com","ip":"192.168.128.113","pid":13982},"userFields":{"ApplicationId":"PROFAPP_001","RequestTrackingId":"RetrieveTBProfileToken-6066477"},"source":"DataAccess\/FetchActiveSessionToken.process","msg":"FetchActiveSessionToken process ended", "type": {"hello": "shouldn't work"}, "id": "2"}
diff --git a/filebeat/tests/system/config/filebeat.yml.j2 b/filebeat/tests/system/config/filebeat.yml.j2
index 938e9e6a9c63..0c48b34ebc24 100644
--- a/filebeat/tests/system/config/filebeat.yml.j2
+++ b/filebeat/tests/system/config/filebeat.yml.j2
@@ -76,6 +76,7 @@ filebeat.{{input_config | default("inputs")}}:
     {% if json.overwrite_keys %}overwrite_keys: true{% endif %}
     {% if json.add_error_key %}add_error_key: true{% endif %}
     {% if json.ignore_decoding_error %}ignore_decoding_error: true{% endif %}
+    {% if json.document_id %}document_id: {{json.document_id}}{% endif %}
   {% endif %}
 
   {% if multiline %}
diff --git a/filebeat/tests/system/test_json.py b/filebeat/tests/system/test_json.py
index 0fec0c680b51..04794e5ccee2 100644
--- a/filebeat/tests/system/test_json.py
+++ b/filebeat/tests/system/test_json.py
@@ -230,6 +230,34 @@ def test_type_in_message(self):
         assert output[2]["error.message"] == \
             "type not overwritten (not string)"
 
+    def test_id_in_message(self):
+        """
+        Extract document ID from json contents.
+        """
+        self.render_config_template(
+            path=os.path.abspath(self.working_dir) + "/log/*",
+            json=dict(
+                message_key="msg",
+                document_id="id",
+            ),
+        )
+        os.mkdir(self.working_dir + "/log/")
+        self.copy_files(["logs/json_id.log"],
+                        target_dir="log")
+        proc = self.start_beat()
+        self.wait_until(
+            lambda: self.output_has(lines=3),
+            max_timeout=10)
+        proc.check_kill_and_wait()
+
+        output = self.read_output()
+
+        assert len(output) == 3
+        for i in xrange(len(output)):
+            assert("@metadata.id" in output[i])
+            assert(output[i]["@metadata.id"] == str(i))
+            assert("json.id" not in output[i])
+
     def test_with_generic_filtering(self):
         """
         It should work fine to combine JSON decoding with
diff --git a/libbeat/reader/readjson/json.go b/libbeat/reader/readjson/json.go
index 72bea9cea359..a669b3f49ae0 100644
--- a/libbeat/reader/readjson/json.go
+++ b/libbeat/reader/readjson/json.go
@@ -114,7 +114,7 @@ func createJSONError(message string) common.MapStr {
 // respecting the KeysUnderRoot and OverwriteKeys configuration options.
 // If MessageKey is defined, the Text value from the event always
 // takes precedence.
-func MergeJSONFields(data common.MapStr, jsonFields common.MapStr, text *string, config Config) time.Time {
+func MergeJSONFields(data common.MapStr, jsonFields common.MapStr, text *string, config Config) (string, time.Time) {
 	// The message key might have been modified by multiline
 	if len(config.MessageKey) > 0 && text != nil {
 		jsonFields[config.MessageKey] = *text
@@ -127,6 +127,16 @@ func MergeJSONFields(data common.MapStr, jsonFields common.MapStr, text *string,
 		data["message"] = *text
 	}
 
+	var id string
+	if key := config.DocumentID; key != "" {
+		if tmp, err := jsonFields.GetValue(key); err == nil {
+			if v, ok := tmp.(string); ok {
+				id = v
+				jsonFields.Delete(key)
+			}
+		}
+	}
+
 	if config.KeysUnderRoot {
 		// Delete existing json key
 		delete(data, "json")
@@ -147,7 +157,7 @@ func MergeJSONFields(data common.MapStr, jsonFields common.MapStr, text *string,
 		}
 		jsontransform.WriteJSONKeys(event, jsonFields, config.OverwriteKeys, config.AddErrorKey)
 
-		return event.Timestamp
+		return id, event.Timestamp
 	}
-	return time.Time{}
+	return id, time.Time{}
 }
diff --git a/libbeat/reader/readjson/json_config.go b/libbeat/reader/readjson/json_config.go
index a95b9db08447..5469f00a3c6a 100644
--- a/libbeat/reader/readjson/json_config.go
+++ b/libbeat/reader/readjson/json_config.go
@@ -20,6 +20,7 @@ package readjson
 // Config holds the options a JSON reader.
 type Config struct {
 	MessageKey          string `config:"message_key"`
+	DocumentID          string `config:"document_id"`
 	KeysUnderRoot       bool   `config:"keys_under_root"`
 	OverwriteKeys       bool   `config:"overwrite_keys"`
 	AddErrorKey         bool   `config:"add_error_key"`
diff --git a/libbeat/reader/readjson/json_test.go b/libbeat/reader/readjson/json_test.go
index 5f4deebd2bee..d6f82585e492 100644
--- a/libbeat/reader/readjson/json_test.go
+++ b/libbeat/reader/readjson/json_test.go
@@ -199,17 +199,15 @@ func TestAddJSONFields(t *testing.T) {
 
 	now := time.Now().UTC()
 
-	tests := []struct {
-		Name              string
+	tests := map[string]struct {
 		Data              common.MapStr
 		Text              *string
 		JSONConfig        Config
 		ExpectedItems     common.MapStr
 		ExpectedTimestamp time.Time
+		ExpectedID        string
 	}{
-		{
-			// by default, don't overwrite keys
-			Name:       "default: do not overwrite",
+		"default: do not overwrite": {
 			Data:       common.MapStr{"type": "test_type", "json": common.MapStr{"type": "test", "text": "hello"}},
 			Text:       &text,
 			JSONConfig: Config{KeysUnderRoot: true},
@@ -219,9 +217,7 @@ func TestAddJSONFields(t *testing.T) {
 			},
 			ExpectedTimestamp: time.Time{},
 		},
-		{
-			// overwrite keys if asked
-			Name:       "overwrite keys if configured",
+		"overwrite keys if configured": {
 			Data:       common.MapStr{"type": "test_type", "json": common.MapStr{"type": "test", "text": "hello"}},
 			Text:       &text,
 			JSONConfig: Config{KeysUnderRoot: true, OverwriteKeys: true},
@@ -231,9 +227,8 @@ func TestAddJSONFields(t *testing.T) {
 			},
 			ExpectedTimestamp: time.Time{},
 		},
-		{
+		"use json namespace w/o keys_under_root": {
 			// without keys_under_root, put everything in a json key
-			Name:       "use json namespace w/o keys_under_root",
 			Data:       common.MapStr{"type": "test_type", "json": common.MapStr{"type": "test", "text": "hello"}},
 			Text:       &text,
 			JSONConfig: Config{},
@@ -242,9 +237,9 @@ func TestAddJSONFields(t *testing.T) {
 			},
 			ExpectedTimestamp: time.Time{},
 		},
-		{
+
+		"write result to message_key field": {
 			// when MessageKey is defined, the Text overwrites the value of that key
-			Name:       "write result to message_key field",
 			Data:       common.MapStr{"type": "test_type", "json": common.MapStr{"type": "test", "text": "hi"}},
 			Text:       &text,
 			JSONConfig: Config{MessageKey: "text"},
@@ -254,10 +249,9 @@ func TestAddJSONFields(t *testing.T) {
 			},
 			ExpectedTimestamp: time.Time{},
 		},
-		{
+		"parse @timestamp": {
 			// when @timestamp is in JSON and overwrite_keys is true, parse it
 			// in a common.Time
-			Name:       "parse @timestamp",
 			Data:       common.MapStr{"@timestamp": now, "type": "test_type", "json": common.MapStr{"type": "test", "@timestamp": "2016-04-05T18:47:18.444Z"}},
 			Text:       &text,
 			JSONConfig: Config{KeysUnderRoot: true, OverwriteKeys: true},
@@ -266,10 +260,9 @@ func TestAddJSONFields(t *testing.T) {
 			},
 			ExpectedTimestamp: time.Time(common.MustParseTime("2016-04-05T18:47:18.444Z")),
 		},
-		{
+		"fail to parse @timestamp": {
 			// when the parsing on @timestamp fails, leave the existing value and add an error key
 			// in a common.Time
-			Name:       "fail to parse @timestamp",
 			Data:       common.MapStr{"@timestamp": common.Time(now), "type": "test_type", "json": common.MapStr{"type": "test", "@timestamp": "2016-04-05T18:47:18.44XX4Z"}},
 			Text:       &text,
 			JSONConfig: Config{KeysUnderRoot: true, OverwriteKeys: true, AddErrorKey: true},
@@ -279,10 +272,10 @@ func TestAddJSONFields(t *testing.T) {
 			},
 			ExpectedTimestamp: time.Time{},
 		},
-		{
+
+		"wrong @timestamp format": {
 			// when the @timestamp has the wrong type, leave the existing value and add an error key
 			// in a common.Time
-			Name:       "wrong @timestamp format",
 			Data:       common.MapStr{"@timestamp": common.Time(now), "type": "test_type", "json": common.MapStr{"type": "test", "@timestamp": 42}},
 			Text:       &text,
 			JSONConfig: Config{KeysUnderRoot: true, OverwriteKeys: true, AddErrorKey: true},
@@ -292,9 +285,8 @@ func TestAddJSONFields(t *testing.T) {
 			},
 			ExpectedTimestamp: time.Time{},
 		},
-		{
+		"ignore non-string type field": {
 			// if overwrite_keys is true, but the `type` key in json is not a string, ignore it
-			Name:       "ignore non-string type field",
 			Data:       common.MapStr{"type": "test_type", "json": common.MapStr{"type": 42}},
 			Text:       &text,
 			JSONConfig: Config{KeysUnderRoot: true, OverwriteKeys: true, AddErrorKey: true},
@@ -304,9 +296,9 @@ func TestAddJSONFields(t *testing.T) {
 			},
 			ExpectedTimestamp: time.Time{},
 		},
-		{
+
+		"ignore empty type field": {
 			// if overwrite_keys is true, but the `type` key in json is empty, ignore it
-			Name:       "ignore empty type field",
 			Data:       common.MapStr{"type": "test_type", "json": common.MapStr{"type": ""}},
 			Text:       &text,
 			JSONConfig: Config{KeysUnderRoot: true, OverwriteKeys: true, AddErrorKey: true},
@@ -316,9 +308,8 @@ func TestAddJSONFields(t *testing.T) {
 			},
 			ExpectedTimestamp: time.Time{},
 		},
-		{
+		"ignore type names starting with underscore": {
 			// if overwrite_keys is true, but the `type` key in json starts with _, ignore it
-			Name:       "ignore type names starting with underscore",
 			Data:       common.MapStr{"@timestamp": common.Time(now), "type": "test_type", "json": common.MapStr{"type": "_type"}},
 			Text:       &text,
 			JSONConfig: Config{KeysUnderRoot: true, OverwriteKeys: true, AddErrorKey: true},
@@ -328,9 +319,7 @@ func TestAddJSONFields(t *testing.T) {
 			},
 			ExpectedTimestamp: time.Time{},
 		},
-		{
-			// if AddErrorKey is false, err should not be set.
-			Name:       "ignore type names starting with underscore",
+		"do not set error if AddErrorKey is false": {
 			Data:       common.MapStr{"@timestamp": common.Time(now), "type": "test_type", "json": common.MapStr{"type": "_type"}},
 			Text:       &text,
 			JSONConfig: Config{KeysUnderRoot: true, OverwriteKeys: true, AddErrorKey: false},
@@ -340,22 +329,35 @@ func TestAddJSONFields(t *testing.T) {
 			},
 			ExpectedTimestamp: time.Time{},
 		},
+		"extract event id": {
+			// if document_id is set, extract the ID from the event
+			Data:       common.MapStr{"@timestamp": common.Time(now), "json": common.MapStr{"id": "test_id"}},
+			JSONConfig: Config{DocumentID: "id"},
+			ExpectedID: "test_id",
+		},
+		"extract event id with wrong type": {
+			// if document_id is set, extract the ID from the event
+			Data:       common.MapStr{"@timestamp": common.Time(now), "json": common.MapStr{"id": 42}},
+			JSONConfig: Config{DocumentID: "id"},
+			ExpectedID: "",
+		},
 	}
 
-	for _, test := range tests {
-		t.Run(test.Name, func(t *testing.T) {
+	for name, test := range tests {
+		t.Run(name, func(t *testing.T) {
 			var jsonFields common.MapStr
 			if fields, ok := test.Data["json"]; ok {
 				jsonFields = fields.(common.MapStr)
 			}
 
-			ts := MergeJSONFields(test.Data, jsonFields, test.Text, test.JSONConfig)
+			id, ts := MergeJSONFields(test.Data, jsonFields, test.Text, test.JSONConfig)
 
 			t.Log("Executing test:", test)
 			for k, v := range test.ExpectedItems {
 				assert.Equal(t, v, test.Data[k])
 			}
 			assert.Equal(t, test.ExpectedTimestamp, ts)
+			assert.Equal(t, test.ExpectedID, id)
 		})
 	}
 }