diff --git a/api/client/container/commit.go b/api/client/container/commit.go
index 9c6525898e..eb23b168d7 100644
--- a/api/client/container/commit.go
+++ b/api/client/container/commit.go
@@ -1,7 +1,6 @@
 package container
 
 import (
-	"encoding/json"
 	"fmt"
 
 	"golang.org/x/net/context"
@@ -10,7 +9,6 @@ import (
 	"github.com/docker/docker/cli"
 	dockeropts "github.com/docker/docker/opts"
 	"github.com/docker/engine-api/types"
-	containertypes "github.com/docker/engine-api/types/container"
 	"github.com/spf13/cobra"
 )
 
@@ -22,7 +20,6 @@ type commitOptions struct {
 	comment string
 	author  string
 	changes dockeropts.ListOpts
-	config  string
 }
 
 // NewCommitCommand creates a new cobra.Command for `docker commit`
@@ -53,10 +50,6 @@ func NewCommitCommand(dockerCli *client.DockerCli) *cobra.Command {
 	opts.changes = dockeropts.NewListOpts(nil)
 	flags.VarP(&opts.changes, "change", "c", "Apply Dockerfile instruction to the created image")
 
-	// FIXME: --run is deprecated, it will be replaced with inline Dockerfile commands.
-	flags.StringVar(&opts.config, "run", "", "This option is deprecated and will be removed in a future version in favor of inline Dockerfile-compatible commands")
-	flags.MarkDeprecated("run", "it will be replaced with inline Dockerfile commands.")
-
 	return cmd
 }
 
@@ -66,21 +59,12 @@ func runCommit(dockerCli *client.DockerCli, opts *commitOptions) error {
 	name := opts.container
 	reference := opts.reference
 
-	var config *containertypes.Config
-	if opts.config != "" {
-		config = &containertypes.Config{}
-		if err := json.Unmarshal([]byte(opts.config), config); err != nil {
-			return err
-		}
-	}
-
 	options := types.ContainerCommitOptions{
 		Reference: reference,
 		Comment:   opts.comment,
 		Author:    opts.author,
 		Changes:   opts.changes.GetAll(),
 		Pause:     opts.pause,
-		Config:    config,
 	}
 
 	response, err := dockerCli.Client().ContainerCommit(ctx, name, options)
diff --git a/docs/deprecated.md b/docs/deprecated.md
index 668d8e89b4..907092c6a4 100644
--- a/docs/deprecated.md
+++ b/docs/deprecated.md
@@ -172,6 +172,15 @@ The single-dash (`-help`) was removed, in favor of the double-dash `--help`
     docker -help
     docker [COMMAND] -help
 
+### `--run` flag on docker commit
+
+**Deprecated In Release: [v0.10.0](https://github.com/docker/docker/releases/tag/v0.10.0)**
+
+**Removed In Release: [v1.13.0](https://github.com/docker/docker/releases/)**
+
+The flag `--run` of the docker commit (and its short version `-run`) were deprecated in favor 
+of the `--changes` flag that allows to pass `Dockerfile` commands.
+
 
 ### Interacting with V1 registries
 
@@ -186,3 +195,4 @@ Since 1.9, Docker Content Trust Offline key has been renamed to Root key and the
 
 - DOCKER_CONTENT_TRUST_OFFLINE_PASSPHRASE is now named DOCKER_CONTENT_TRUST_ROOT_PASSPHRASE
 - DOCKER_CONTENT_TRUST_TAGGING_PASSPHRASE is now named DOCKER_CONTENT_TRUST_REPOSITORY_PASSPHRASE
+
diff --git a/integration-cli/docker_cli_build_test.go b/integration-cli/docker_cli_build_test.go
index a115a7d672..fcb2a672cd 100644
--- a/integration-cli/docker_cli_build_test.go
+++ b/integration-cli/docker_cli_build_test.go
@@ -438,72 +438,6 @@ func (s *DockerSuite) TestBuildEnvOverwrite(c *check.C) {
 
 }
 
-func (s *DockerSuite) TestBuildOnBuildForbiddenMaintainerInSourceImage(c *check.C) {
-	name := "testbuildonbuildforbiddenmaintainerinsourceimage"
-
-	out, _ := dockerCmd(c, "create", "busybox", "true")
-
-	cleanedContainerID := strings.TrimSpace(out)
-
-	dockerCmd(c, "commit", "--run", "{\"OnBuild\":[\"MAINTAINER docker.io\"]}", cleanedContainerID, "onbuild")
-
-	_, err := buildImage(name,
-		`FROM onbuild`,
-		true)
-	if err != nil {
-		if !strings.Contains(err.Error(), "maintainer isn't allowed as an ONBUILD trigger") {
-			c.Fatalf("Wrong error %v, must be about MAINTAINER and ONBUILD in source image", err)
-		}
-	} else {
-		c.Fatal("Error must not be nil")
-	}
-
-}
-
-func (s *DockerSuite) TestBuildOnBuildForbiddenFromInSourceImage(c *check.C) {
-	name := "testbuildonbuildforbiddenfrominsourceimage"
-
-	out, _ := dockerCmd(c, "create", "busybox", "true")
-
-	cleanedContainerID := strings.TrimSpace(out)
-
-	dockerCmd(c, "commit", "--run", "{\"OnBuild\":[\"FROM busybox\"]}", cleanedContainerID, "onbuild")
-
-	_, err := buildImage(name,
-		`FROM onbuild`,
-		true)
-	if err != nil {
-		if !strings.Contains(err.Error(), "from isn't allowed as an ONBUILD trigger") {
-			c.Fatalf("Wrong error %v, must be about FROM and ONBUILD in source image", err)
-		}
-	} else {
-		c.Fatal("Error must not be nil")
-	}
-
-}
-
-func (s *DockerSuite) TestBuildOnBuildForbiddenChainedInSourceImage(c *check.C) {
-	name := "testbuildonbuildforbiddenchainedinsourceimage"
-
-	out, _ := dockerCmd(c, "create", "busybox", "true")
-
-	cleanedContainerID := strings.TrimSpace(out)
-
-	dockerCmd(c, "commit", "--run", "{\"OnBuild\":[\"ONBUILD RUN ls\"]}", cleanedContainerID, "onbuild")
-
-	_, err := buildImage(name,
-		`FROM onbuild`,
-		true)
-	if err != nil {
-		if !strings.Contains(err.Error(), "Chaining ONBUILD via `ONBUILD ONBUILD` isn't allowed") {
-			c.Fatalf("Wrong error %v, must be about chaining ONBUILD in source image", err)
-		}
-	} else {
-		c.Fatal("Error must not be nil")
-	}
-
-}
-
 func (s *DockerSuite) TestBuildOnBuildCmdEntrypointJSON(c *check.C) {
 	name1 := "onbuildcmd"
 	name2 := "onbuildgenerated"
diff --git a/integration-cli/docker_cli_commit_test.go b/integration-cli/docker_cli_commit_test.go
index 086a203124..0a95c92f41 100644
--- a/integration-cli/docker_cli_commit_test.go
+++ b/integration-cli/docker_cli_commit_test.go
@@ -144,46 +144,3 @@ func (s *DockerSuite) TestCommitChange(c *check.C) {
 		}
 	}
 }
-
-// TODO: commit --run is deprecated, remove this once --run is removed
-func (s *DockerSuite) TestCommitMergeConfigRun(c *check.C) {
-	testRequires(c, DaemonIsLinux)
-	name := "commit-test"
-	out, _ := dockerCmd(c, "run", "-d", "-e=FOO=bar", "busybox", "/bin/sh", "-c", "echo testing > /tmp/foo")
-	id := strings.TrimSpace(out)
-
-	dockerCmd(c, "commit", `--run={"Cmd": ["cat", "/tmp/foo"]}`, id, "commit-test")
-
-	out, _ = dockerCmd(c, "run", "--name", name, "commit-test")
-	//run config in committed container was not merged
-	c.Assert(strings.TrimSpace(out), checker.Equals, "testing")
-
-	type cfg struct {
-		Env []string
-		Cmd []string
-	}
-	config1 := cfg{}
-	inspectFieldAndMarshall(c, id, "Config", &config1)
-
-	config2 := cfg{}
-	inspectFieldAndMarshall(c, name, "Config", &config2)
-
-	// Env has at least PATH loaded as well here, so let's just grab the FOO one
-	var env1, env2 string
-	for _, e := range config1.Env {
-		if strings.HasPrefix(e, "FOO") {
-			env1 = e
-			break
-		}
-	}
-	for _, e := range config2.Env {
-		if strings.HasPrefix(e, "FOO") {
-			env2 = e
-			break
-		}
-	}
-
-	if len(config1.Env) != len(config2.Env) || env1 != env2 && env2 != "" {
-		c.Fatalf("expected envs to match: %v - %v", config1.Env, config2.Env)
-	}
-}