diff --git a/src/commonMain/kotlin/io/github/optimumcode/json/schema/internal/SchemaLoader.kt b/src/commonMain/kotlin/io/github/optimumcode/json/schema/internal/SchemaLoader.kt
index a32c0218..4019e038 100644
--- a/src/commonMain/kotlin/io/github/optimumcode/json/schema/internal/SchemaLoader.kt
+++ b/src/commonMain/kotlin/io/github/optimumcode/json/schema/internal/SchemaLoader.kt
@@ -26,7 +26,7 @@ private const val SCHEMA_PROPERTY: String = "\$schema"
 
 internal class SchemaLoader : JsonSchemaLoader {
   private val references: MutableMap<RefId, AssertionWithPath> = linkedMapOf()
-  private val usedRefs: MutableSet<RefId> = linkedSetOf()
+  private val usedRefs: MutableSet<ReferenceLocation> = linkedSetOf()
 
   override fun register(
     schema: JsonElement,
@@ -67,11 +67,12 @@ internal class SchemaLoader : JsonSchemaLoader {
     draft: SchemaType?,
   ): JsonSchema {
     val assertion: JsonSchemaAssertion = loadSchemaData(schemaElement, draft, references, usedRefs)
+    validateReferences(references, usedRefs)
     return createSchema(
       LoadResult(
         assertion,
         references.toMutableMap(),
-        usedRefs.toMutableSet(),
+        usedRefs.mapTo(hashSetOf()) { it.refId },
       ),
     )
   }
@@ -107,9 +108,10 @@ internal object IsolatedLoader : JsonSchemaLoader {
     draft: SchemaType?,
   ): JsonSchema {
     val references: MutableMap<RefId, AssertionWithPath> = linkedMapOf()
-    val usedRefs: MutableSet<RefId> = hashSetOf()
+    val usedRefs: MutableSet<ReferenceLocation> = hashSetOf()
     val assertion: JsonSchemaAssertion = loadSchemaData(schemaElement, draft, references, usedRefs)
-    return createSchema(LoadResult(assertion, references, usedRefs))
+    validateReferences(references, usedRefs)
+    return createSchema(LoadResult(assertion, references, usedRefs.mapTo(hashSetOf()) { it.refId }))
   }
 }
 
@@ -117,7 +119,7 @@ private fun loadSchemaData(
   schemaDefinition: JsonElement,
   defaultType: SchemaType?,
   references: MutableMap<RefId, AssertionWithPath>,
-  usedRefs: MutableSet<RefId>,
+  usedRefs: MutableSet<ReferenceLocation>,
   externalUri: Uri? = null,
 ): JsonSchemaAssertion {
   val schemaType = extractSchemaType(schemaDefinition, defaultType)
@@ -138,12 +140,18 @@ private fun loadSchemaData(
       }
   val schemaAssertion = loadSchema(schemaDefinition, context)
   references.putAll(isolatedReferences)
-  context.usedRef.mapTo(usedRefs) { it.refId }
+  usedRefs.addAll(context.usedRef)
+  return schemaAssertion
+}
+
+private fun validateReferences(
+  references: Map<RefId, AssertionWithPath>,
+  usedRefs: Set<ReferenceLocation>,
+) {
   ReferenceValidator.validateReferences(
     references.mapValues { it.value.run { PointerWithBaseId(this.baseId, schemaPath) } },
-    context.usedRef,
+    usedRefs,
   )
-  return schemaAssertion
 }
 
 private fun createSchema(result: LoadResult): JsonSchema {
diff --git a/src/commonTest/kotlin/io/github/optimumcode/json/schema/base/JsonSchemaLoaderTest.kt b/src/commonTest/kotlin/io/github/optimumcode/json/schema/base/JsonSchemaLoaderTest.kt
index 79526546..cf81ba62 100644
--- a/src/commonTest/kotlin/io/github/optimumcode/json/schema/base/JsonSchemaLoaderTest.kt
+++ b/src/commonTest/kotlin/io/github/optimumcode/json/schema/base/JsonSchemaLoaderTest.kt
@@ -5,6 +5,8 @@ import io.github.optimumcode.json.schema.ErrorCollector
 import io.github.optimumcode.json.schema.JsonSchemaLoader
 import io.github.optimumcode.json.schema.ValidationError
 import io.kotest.assertions.assertSoftly
+import io.kotest.assertions.throwables.shouldNotThrowAnyUnit
+import io.kotest.assertions.throwables.shouldThrow
 import io.kotest.assertions.withClue
 import io.kotest.core.spec.style.FunSpec
 import io.kotest.matchers.collections.shouldContainExactly
@@ -161,5 +163,53 @@ class JsonSchemaLoaderTest : FunSpec() {
           }
         }
       }
+
+    test("does not report missing refs when schema is registered") {
+      shouldNotThrowAnyUnit {
+        JsonSchemaLoader.create()
+          .register(
+            """
+            {
+              "id": "https://test.com/a",
+              "properties": {
+                "anotherName": {
+                  "${KEY}ref": "https://test.com/b#/properties/name"
+                }
+              }
+            }
+            """.trimIndent(),
+          )
+      }
+    }
+
+    test("reports missing refs when schema is created from definition") {
+      shouldThrow<IllegalArgumentException> {
+        JsonSchemaLoader.create()
+          .register(
+            """
+            {
+              "${KEY}id": "https://test.com/a",
+              "properties": {
+                "anotherName": {
+                  "${KEY}ref": "https://test.com/b#/properties/name"
+                }
+              }
+            }
+            """.trimIndent(),
+          ).fromDefinition(
+            """
+            {
+              "${KEY}id": "https://test.com/c",
+              "properties": {
+                "subName": {
+                  "${KEY}ref": "https://test.com/a#/properties/anotherName"
+                }
+              }
+            }
+            """.trimIndent(),
+          )
+      }.message shouldBe "cannot resolve references: " +
+        "{\"https://test.com/b#/properties/name\": [\"/properties/anotherName\"]}"
+    }
   }
 }
\ No newline at end of file
diff --git a/test-suites/src/commonTest/kotlin/io/github/optimumcode/json/schema/suite/AbstractSchemaTestSuite.kt b/test-suites/src/commonTest/kotlin/io/github/optimumcode/json/schema/suite/AbstractSchemaTestSuite.kt
index 6d26ba1b..4c7aeb06 100644
--- a/test-suites/src/commonTest/kotlin/io/github/optimumcode/json/schema/suite/AbstractSchemaTestSuite.kt
+++ b/test-suites/src/commonTest/kotlin/io/github/optimumcode/json/schema/suite/AbstractSchemaTestSuite.kt
@@ -133,7 +133,7 @@ private fun FunSpec.executeFromDirectory(
       JsonSchemaLoader.create()
         .apply {
           SchemaType.entries.forEach(::registerWellKnown)
-          for ((uri, schema) in remoteSchemas.entries.reversed()) {
+          for ((uri, schema) in remoteSchemas) {
             if (uri.contains("draft4", ignoreCase = true)) {
               // skip draft4 schemas
               continue