diff --git a/execdriver/driver.go b/execdriver/driver.go
index 8b5dd5ccc7..d64c08fa6c 100644
--- a/execdriver/driver.go
+++ b/execdriver/driver.go
@@ -53,6 +53,7 @@ type InitArgs struct {
 	Driver     string
 	Console    string
 	Pipe       int
+	Root       string
 }
 
 // Driver specific information based on
diff --git a/execdriver/native/driver.go b/execdriver/native/driver.go
index 16e5ea1b49..6236950476 100644
--- a/execdriver/native/driver.go
+++ b/execdriver/native/driver.go
@@ -25,9 +25,9 @@ func init() {
 	execdriver.RegisterInitFunc(DriverName, func(args *execdriver.InitArgs) error {
 		var (
 			container *libcontainer.Container
-			ns        = nsinit.NewNsInit(&nsinit.DefaultCommandFactory{}, &nsinit.DefaultStateWriter{})
+			ns        = nsinit.NewNsInit(&nsinit.DefaultCommandFactory{}, &nsinit.DefaultStateWriter{args.Root})
 		)
-		f, err := os.Open("container.json")
+		f, err := os.Open(filepath.Join(args.Root, "container.json"))
 		if err != nil {
 			return err
 		}
@@ -57,6 +57,9 @@ type driver struct {
 }
 
 func NewDriver(root string) (*driver, error) {
+	if err := os.MkdirAll(root, 0655); err != nil {
+		return nil, err
+	}
 	return &driver{
 		root: root,
 	}, nil
@@ -66,14 +69,18 @@ func (d *driver) Run(c *execdriver.Command, pipes *execdriver.Pipes, startCallba
 	var (
 		term        nsinit.Terminal
 		container   = createContainer(c)
-		factory     = &dockerCommandFactory{c}
+		factory     = &dockerCommandFactory{c: c, driver: d}
 		stateWriter = &dockerStateWriter{
 			callback: startCallback,
 			c:        c,
-			dsw:      &nsinit.DefaultStateWriter{c.Rootfs},
+			dsw:      &nsinit.DefaultStateWriter{filepath.Join(d.root, c.ID)},
 		}
-		ns = nsinit.NewNsInit(factory, stateWriter)
+		ns   = nsinit.NewNsInit(factory, stateWriter)
+		args = append([]string{c.Entrypoint}, c.Arguments...)
 	)
+	if err := d.createContainerRoot(c.ID); err != nil {
+		return -1, err
+	}
 	if c.Tty {
 		term = &dockerTtyTerm{
 			pipes: pipes,
@@ -84,10 +91,9 @@ func (d *driver) Run(c *execdriver.Command, pipes *execdriver.Pipes, startCallba
 		}
 	}
 	c.Terminal = term
-	if err := writeContainerFile(container, c.Rootfs); err != nil {
+	if err := d.writeContainerFile(container, c.ID); err != nil {
 		return -1, err
 	}
-	args := append([]string{c.Entrypoint}, c.Arguments...)
 	return ns.Exec(container, term, args)
 }
 
@@ -98,9 +104,9 @@ func (d *driver) Kill(p *execdriver.Command, sig int) error {
 func (d *driver) Restore(c *execdriver.Command) error {
 	var (
 		nspid int
-		p     = filepath.Join(d.root, "containers", c.ID, "root", ".nspid")
+		path  = filepath.Join(d.root, c.ID, "pid")
 	)
-	f, err := os.Open(p)
+	f, err := os.Open(path)
 	if err != nil {
 		return err
 	}
@@ -109,7 +115,7 @@ func (d *driver) Restore(c *execdriver.Command) error {
 		return err
 	}
 	f.Close()
-	defer os.Remove(p)
+	defer os.Remove(path)
 
 	proc, err := os.FindProcess(nspid)
 	if err != nil {
@@ -167,12 +173,16 @@ func (d *driver) GetPidsForContainer(id string) ([]int, error) {
 	return pids, nil
 }
 
-func writeContainerFile(container *libcontainer.Container, rootfs string) error {
+func (d *driver) writeContainerFile(container *libcontainer.Container, id string) error {
 	data, err := json.Marshal(container)
 	if err != nil {
 		return err
 	}
-	return ioutil.WriteFile(filepath.Join(rootfs, "container.json"), data, 0755)
+	return ioutil.WriteFile(filepath.Join(d.root, id, "container.json"), data, 0655)
+}
+
+func (d *driver) createContainerRoot(id string) error {
+	return os.MkdirAll(filepath.Join(d.root, id), 0655)
 }
 
 func getEnv(key string, env []string) string {
@@ -186,7 +196,8 @@ func getEnv(key string, env []string) string {
 }
 
 type dockerCommandFactory struct {
-	c *execdriver.Command
+	c      *execdriver.Command
+	driver *driver
 }
 
 // createCommand will return an exec.Cmd with the Cloneflags set to the proper namespaces
@@ -202,6 +213,7 @@ func (d *dockerCommandFactory) Create(container *libcontainer.Container, console
 		"-driver", DriverName,
 		"-console", console,
 		"-pipe", fmt.Sprint(syncFd),
+		"-root", filepath.Join(d.driver.root, d.c.ID),
 	}, args...)
 	d.c.SysProcAttr = &syscall.SysProcAttr{
 		Cloneflags: uintptr(nsinit.GetNamespaceFlags(container.Namespaces)),
diff --git a/execdriver/native/info.go b/execdriver/native/info.go
index a2ab7f2a0a..5223feee83 100644
--- a/execdriver/native/info.go
+++ b/execdriver/native/info.go
@@ -14,8 +14,7 @@ type info struct {
 // .nspid file for a container.  If the file exists then the
 // container is currently running
 func (i *info) IsRunning() bool {
-	p := filepath.Join(i.driver.root, "containers", i.ID, "root", ".nspid")
-	if _, err := os.Stat(p); err == nil {
+	if _, err := os.Stat(filepath.Join(i.driver.root, i.ID, "pid")); err == nil {
 		return true
 	}
 	return false
diff --git a/pkg/libcontainer/nsinit/execin.go b/pkg/libcontainer/nsinit/execin.go
index 306250cf9b..253fbdcea4 100644
--- a/pkg/libcontainer/nsinit/execin.go
+++ b/pkg/libcontainer/nsinit/execin.go
@@ -42,7 +42,7 @@ func (ns *linuxNs) ExecIn(container *libcontainer.Container, nspid int, args []s
 
 	// if the container has a new pid and mount namespace we need to
 	// remount proc and sys to pick up the changes
-	if container.Namespaces.Contains("CLONE_NEWNS") && container.Namespaces.Contains("CLONE_NEWPID") {
+	if container.Namespaces.Contains("NEWNS") && container.Namespaces.Contains("NEWPID") {
 		pid, err := system.Fork()
 		if err != nil {
 			return -1, err
diff --git a/pkg/libcontainer/nsinit/nsinit/main.go b/pkg/libcontainer/nsinit/nsinit/main.go
index e385e7fb70..e6b020b74b 100644
--- a/pkg/libcontainer/nsinit/nsinit/main.go
+++ b/pkg/libcontainer/nsinit/nsinit/main.go
@@ -9,12 +9,13 @@ import (
 	"io/ioutil"
 	"log"
 	"os"
+	"path/filepath"
 	"strconv"
 )
 
 var (
-	console string
-	pipeFd  int
+	root, console string
+	pipeFd        int
 )
 
 var (
@@ -25,6 +26,7 @@ var (
 func registerFlags() {
 	flag.StringVar(&console, "console", "", "console (pty slave) path")
 	flag.IntVar(&pipeFd, "pipe", 0, "sync pipe fd")
+	flag.StringVar(&root, "root", ".", "root for storing configuration data")
 
 	flag.Parse()
 }
@@ -84,7 +86,7 @@ func main() {
 }
 
 func loadContainer() (*libcontainer.Container, error) {
-	f, err := os.Open("container.json")
+	f, err := os.Open(filepath.Join(root, "container.json"))
 	if err != nil {
 		return nil, err
 	}
@@ -98,7 +100,7 @@ func loadContainer() (*libcontainer.Container, error) {
 }
 
 func readPid() (int, error) {
-	data, err := ioutil.ReadFile(".nspid")
+	data, err := ioutil.ReadFile(filepath.Join(root, "pid"))
 	if err != nil {
 		return -1, err
 	}
@@ -110,5 +112,5 @@ func readPid() (int, error) {
 }
 
 func newNsInit() (nsinit.NsInit, error) {
-	return nsinit.NewNsInit(&nsinit.DefaultCommandFactory{}, &nsinit.DefaultStateWriter{}), nil
+	return nsinit.NewNsInit(&nsinit.DefaultCommandFactory{}, &nsinit.DefaultStateWriter{root}), nil
 }
diff --git a/pkg/libcontainer/nsinit/state.go b/pkg/libcontainer/nsinit/state.go
index 5c719e1c54..af38008c03 100644
--- a/pkg/libcontainer/nsinit/state.go
+++ b/pkg/libcontainer/nsinit/state.go
@@ -18,11 +18,11 @@ type DefaultStateWriter struct {
 	Root string
 }
 
-// writePidFile writes the namespaced processes pid to .nspid in the rootfs for the container
+// writePidFile writes the namespaced processes pid to pid in the rootfs for the container
 func (d *DefaultStateWriter) WritePid(pid int) error {
-	return ioutil.WriteFile(filepath.Join(d.Root, ".nspid"), []byte(fmt.Sprint(pid)), 0655)
+	return ioutil.WriteFile(filepath.Join(d.Root, "pid"), []byte(fmt.Sprint(pid)), 0655)
 }
 
 func (d *DefaultStateWriter) DeletePid() error {
-	return os.Remove(filepath.Join(d.Root, ".nspid"))
+	return os.Remove(filepath.Join(d.Root, "pid"))
 }
diff --git a/runtime.go b/runtime.go
index 1a95ad6270..c062578a31 100644
--- a/runtime.go
+++ b/runtime.go
@@ -711,7 +711,7 @@ func NewRuntimeFromDirectory(config *DaemonConfig, eng *engine.Engine) (*Runtime
 	case "lxc":
 		ed, err = lxc.NewDriver(config.Root, sysInfo.AppArmor)
 	case "native":
-		ed, err = native.NewDriver(config.Root)
+		ed, err = native.NewDriver(path.Join(config.Root, "native"))
 	default:
 		return nil, fmt.Errorf("unknown exec driver %s", config.ExecDriver)
 	}
diff --git a/sysinit/sysinit.go b/sysinit/sysinit.go
index 3f2b0b6066..c84c05982c 100644
--- a/sysinit/sysinit.go
+++ b/sysinit/sysinit.go
@@ -55,6 +55,7 @@ func SysInit() {
 		driver     = flag.String("driver", "", "exec driver")
 		pipe       = flag.Int("pipe", 0, "sync pipe fd")
 		console    = flag.String("console", "", "console (pty slave) path")
+		root       = flag.String("root", ".", "root path for configuration files")
 	)
 	flag.Parse()
 
@@ -82,6 +83,7 @@ func SysInit() {
 		Driver:     *driver,
 		Console:    *console,
 		Pipe:       *pipe,
+		Root:       *root,
 	}
 
 	if err := executeProgram(args); err != nil {