diff --git a/cmd/init.go b/cmd/init.go
new file mode 100644
index 00000000..fd9b9ef6
--- /dev/null
+++ b/cmd/init.go
@@ -0,0 +1,25 @@
+package cmd
+
+import (
+	"github.com/rs/zerolog/log"
+	"github.com/spf13/cobra"
+
+	"github.com/mykso/myks/internal/myks"
+)
+
+func init() {
+	cmd := &cobra.Command{
+		Use:   "init",
+		Short: "Initialize new myks project",
+		Long:  "Initialize new myks project",
+		Run: func(cmd *cobra.Command, args []string) {
+			g := myks.New(".")
+
+			if err := g.Bootstrap(); err != nil {
+				log.Fatal().Err(err).Msg("Failed to initialize project")
+			}
+		},
+	}
+
+	rootCmd.AddCommand(cmd)
+}
diff --git a/internal/myks/assets/env-data.ytt.yaml b/internal/myks/assets/env-data.ytt.yaml
new file mode 100644
index 00000000..170cb9b9
--- /dev/null
+++ b/internal/myks/assets/env-data.ytt.yaml
@@ -0,0 +1,25 @@
+#! This file define a schema for all ytt data files. It can also contain default values.
+#! Top-level keys are scopes, e.g. application, argocd, environment, helm.
+#! Content of the `application` scope can be freely modified. More scopes can be added.
+#! The `environment`, `helm` and `argocd` scopes are used by myks and should not be modified.
+#! However, more keys can be added to these scopes.
+
+#@data/values-schema
+---
+#! Add here any application-specific data.
+application: {}
+environment:
+  #! Unique identifier of the environment, required by myks.
+  #@schema/validation min_len=1
+  id: ""
+#! Configuration of the step that renders Helm charts.
+helm:
+  #! Used by myks.
+  #! If true, adds `--include-crds` flag to `helm template`.
+  includeCRDs: true
+  #! Used by myks.
+  #! If defined, passed as a value of `--kube-version` for `helm template`.
+  kubeVersion: ""
+  #! Used by myks.
+  #! If defined, passed as a value of `--namespace` for `helm template`.
+  namespace: ""
diff --git a/internal/myks/globe.go b/internal/myks/globe.go
index 1ecdee15..77c44fb0 100644
--- a/internal/myks/globe.go
+++ b/internal/myks/globe.go
@@ -1,6 +1,7 @@
 package myks
 
 import (
+	_ "embed"
 	"fmt"
 	"io"
 	"io/fs"
@@ -11,6 +12,9 @@ import (
 	"github.com/rs/zerolog/log"
 )
 
+//go:embed assets/env-data.ytt.yaml
+var dataSchema []byte
+
 // Define the main structure
 type Globe struct {
 	/// Globe configuration
@@ -132,6 +136,57 @@ func (g *Globe) SyncAndRender() error {
 	})
 }
 
+// Bootstrap creates the initial directory structure and files
+func (g *Globe) Bootstrap() error {
+	return g.createBaseFileStructure()
+}
+
+func (g *Globe) createBaseFileStructure() error {
+	envDir := filepath.Join(g.RootDir, g.EnvironmentBaseDir)
+	protoDir := filepath.Join(g.RootDir, g.PrototypesDir)
+	renderedDir := filepath.Join(g.RootDir, g.RenderedDir)
+	dataSchemaFile := filepath.Join(envDir, g.EnvironmentDataFileName)
+
+	log.Debug().
+		Str("environments directory", envDir).
+		Str("prototypes directory", protoDir).
+		Str("rendered directory", renderedDir).
+		Str("data schema file", dataSchemaFile).
+		Msg("Creating base file structure")
+
+	notCleanErr := fmt.Errorf("Target directory is not clean, aborting")
+
+	if _, err := os.Stat(envDir); err == nil {
+		return notCleanErr
+	}
+	if err := os.MkdirAll(envDir, 0o755); err != nil {
+		return err
+	}
+
+	if _, err := os.Stat(protoDir); err == nil {
+		return notCleanErr
+	}
+	if err := os.MkdirAll(protoDir, 0o755); err != nil {
+		return err
+	}
+
+	if _, err := os.Stat(renderedDir); err == nil {
+		return notCleanErr
+	}
+	if err := os.MkdirAll(renderedDir, 0o755); err != nil {
+		return err
+	}
+
+	if _, err := os.Stat(dataSchemaFile); err == nil {
+		return notCleanErr
+	}
+	if err := os.WriteFile(dataSchemaFile, dataSchema, 0o644); err != nil {
+		return err
+	}
+
+	return nil
+}
+
 func (g *Globe) collectEnvironments(searchPaths []string) {
 	if len(searchPaths) == 0 {
 		searchPaths = []string{g.EnvironmentBaseDir}