diff --git a/cmd/drone-server/static/scripts/controllers/repos.js b/cmd/drone-server/static/scripts/controllers/repos.js
index 0e51f1e13..f150faacc 100644
--- a/cmd/drone-server/static/scripts/controllers/repos.js
+++ b/cmd/drone-server/static/scripts/controllers/repos.js
@@ -119,9 +119,8 @@
 
 
     $scope.encrypt = function (plaintext) {
-      var data = {"DATA": plaintext};
-      repos.encrypt(fullName, data).then(function (payload) {
-        $scope.secure = payload.data["DATA"];
+      repos.encrypt(fullName, plaintext).then(function (payload) {
+        $scope.secure = payload.data;
       }).catch(function (err) {
         $scope.error = err;
       });
diff --git a/cmd/drone-server/static/scripts/services/repos.js b/cmd/drone-server/static/scripts/services/repos.js
index e66048f14..165f90a47 100644
--- a/cmd/drone-server/static/scripts/services/repos.js
+++ b/cmd/drone-server/static/scripts/services/repos.js
@@ -77,10 +77,10 @@
      * Encrypt the set of parameters.
      *
      * @param {string} Name of the repository.
-     * @param {object} Key/Value map of parameters.
+     * @param {string} Plaintext to encrypt.
      */
-    this.encrypt = function (repoName, params) {
-      return $http.post('/api/repos/' + repoName + '/encrypt', params);
+    this.encrypt = function (repoName, plaintext) {
+      return $http.post('/api/repos/' + repoName + '/encrypt', plaintext);
     };
 
     var callback,
diff --git a/cmd/drone-server/static/scripts/views/repos/secure.html b/cmd/drone-server/static/scripts/views/repos/secure.html
index 682300112..7bb7541f5 100644
--- a/cmd/drone-server/static/scripts/views/repos/secure.html
+++ b/cmd/drone-server/static/scripts/views/repos/secure.html
@@ -2,7 +2,7 @@
 <article>
 
 	<p style="  font-size: 16px;
-  margin-bottom: 10px;">Encrypt and store secret variables in your <code>.drone.yml</code> file<p>
+  margin-bottom: 10px;">Encrypt and store secret variables in the <code>.drone.sec</code> file<p>
 	<textarea spellcheck="false" placeholder="Enter a plaintext value here" ng-model="plaintext" style="
   background-color: #eff1f5;
   border-radius:3px;
diff --git a/pkg/queue/worker.go b/pkg/queue/worker.go
index 36c6fe247..3ae07a187 100644
--- a/pkg/queue/worker.go
+++ b/pkg/queue/worker.go
@@ -15,7 +15,8 @@ type Work struct {
 	Build  *common.Build   `json:"build"`
 	Keys   *common.Keypair `json:"keypair"`
 	Netrc  *common.Netrc   `json:"netrc"`
-	Yaml   []byte          `json:"yaml"`
+	Config []byte          `json:"config"`
+	Secret []byte          `json:"secret"`
 }
 
 // represents a worker that has connected
diff --git a/pkg/remote/builtin/github/github.go b/pkg/remote/builtin/github/github.go
index 7876a60b8..5c8192a44 100644
--- a/pkg/remote/builtin/github/github.go
+++ b/pkg/remote/builtin/github/github.go
@@ -163,9 +163,12 @@ func (g *GitHub) Perm(u *common.User, owner, name string) (*common.Perm, error)
 
 // Script fetches the build script (.drone.yml) from the remote
 // repository and returns in string format.
-func (g *GitHub) Script(u *common.User, r *common.Repo, b *common.Build) ([]byte, error) {
+func (g *GitHub) Script(u *common.User, r *common.Repo, b *common.Build) ([]byte, []byte, error) {
 	client := NewClient(g.API, u.Token, g.SkipVerify)
-	return GetFile(client, r.Owner, r.Name, ".drone.yml", b.Commit.Sha)
+
+	cfg, err := GetFile(client, r.Owner, r.Name, ".drone.yml", b.Commit.Sha)
+	sec, _ := GetFile(client, r.Owner, r.Name, ".drone.sec", b.Commit.Sha)
+	return cfg, sec, err
 }
 
 // Netrc returns a .netrc file that can be used to clone
diff --git a/pkg/remote/builtin/gitlab/gitlab.go b/pkg/remote/builtin/gitlab/gitlab.go
index 1244f6268..79a162c8f 100644
--- a/pkg/remote/builtin/gitlab/gitlab.go
+++ b/pkg/remote/builtin/gitlab/gitlab.go
@@ -159,14 +159,16 @@ func (g *Gitlab) Perm(u *common.User, owner, name string) (*common.Perm, error)
 
 // GetScript fetches the build script (.drone.yml) from the remote
 // repository and returns in string format.
-func (g *Gitlab) Script(user *common.User, repo *common.Repo, build *common.Build) ([]byte, error) {
+func (g *Gitlab) Script(user *common.User, repo *common.Repo, build *common.Build) ([]byte, []byte, error) {
 	var client = NewClient(g.URL, user.Token, g.SkipVerify)
 	id, err := GetProjectId(g, client, repo.Owner, repo.Name)
 	if err != nil {
-		return nil, err
+		return nil, nil, err
 	}
 
-	return client.RepoRawFile(id, build.Commit.Sha, ".drone.yml")
+	cfg, err := client.RepoRawFile(id, build.Commit.Sha, ".drone.yml")
+	enc, _ := client.RepoRawFile(id, build.Commit.Sha, ".drone.sec")
+	return cfg, enc, err
 }
 
 // NOTE Currently gitlab doesn't support status for commits and events,
diff --git a/pkg/remote/remote.go b/pkg/remote/remote.go
index 9d6367414..e1d4cd39e 100644
--- a/pkg/remote/remote.go
+++ b/pkg/remote/remote.go
@@ -56,7 +56,7 @@ type Remote interface {
 
 	// Script fetches the build script (.drone.yml) from the remote
 	// repository and returns in string format.
-	Script(u *types.User, r *types.Repo, b *types.Build) ([]byte, error)
+	Script(u *types.User, r *types.Repo, b *types.Build) ([]byte, []byte, error)
 
 	// Status sends the commit status to the remote system.
 	// An example would be the GitHub pull request status.
diff --git a/pkg/runner/builtin/runner.go b/pkg/runner/builtin/runner.go
index 60d98a680..b5227ba91 100644
--- a/pkg/runner/builtin/runner.go
+++ b/pkg/runner/builtin/runner.go
@@ -144,7 +144,8 @@ func (r *Runner) Run(w *queue.Work) error {
 			Repo:      w.Repo,
 			Build:     w.Build,
 			Job:       job,
-			Yaml:      string(w.Yaml),
+			Secret:    string(w.Secret),
+			Config:    string(w.Config),
 		}
 		in, err := json.Marshal(work)
 		if err != nil {
@@ -224,7 +225,8 @@ func (r *Runner) Run(w *queue.Work) error {
 			Repo:      w.Repo,
 			Build:     w.Build,
 			Job:       job,
-			Yaml:      string(w.Yaml),
+			Secret:    string(w.Secret),
+			Config:    string(w.Config),
 		}
 		in, err := json.Marshal(work)
 		if err != nil {
diff --git a/pkg/runner/builtin/worker.go b/pkg/runner/builtin/worker.go
index 409dab6c8..b92894ca3 100644
--- a/pkg/runner/builtin/worker.go
+++ b/pkg/runner/builtin/worker.go
@@ -50,7 +50,8 @@ type work struct {
 	Job       *types.Job       `json:"job"`
 	System    *types.System    `json:"system"`
 	Workspace *types.Workspace `json:"workspace"`
-	Yaml      string           `json:"yaml"`
+	Secret    string           `json:"secret"`
+	Config    string           `json:"config"`
 }
 
 type worker struct {
diff --git a/pkg/server/commits.go b/pkg/server/commits.go
index 870271b87..e0217e01e 100644
--- a/pkg/server/commits.go
+++ b/pkg/server/commits.go
@@ -6,14 +6,10 @@ import (
 	"strconv"
 	"time"
 
-	log "github.com/drone/drone/Godeps/_workspace/src/github.com/Sirupsen/logrus"
 	"github.com/drone/drone/Godeps/_workspace/src/github.com/gin-gonic/gin"
 	"github.com/drone/drone/pkg/queue"
 	common "github.com/drone/drone/pkg/types"
 	"github.com/drone/drone/pkg/utils/httputil"
-	"github.com/drone/drone/pkg/yaml/inject"
-	"github.com/drone/drone/pkg/yaml/secure"
-	// "github.com/gin-gonic/gin/binding"
 )
 
 // GetCommit accepts a request to retrieve a commit
@@ -175,33 +171,22 @@ func RunBuild(c *gin.Context) {
 	}
 
 	// featch the .drone.yml file from the database
-	raw, err := remote.Script(user, repo, build)
+	raw, sec, err := remote.Script(user, repo, build)
 	if err != nil {
 		c.Fail(404, err)
 		return
 	}
 
-	// inject any private parameters into the .drone.yml
-	if repo.Params != nil && len(repo.Params) != 0 {
-		raw = []byte(inject.InjectSafe(string(raw), repo.Params))
-	}
-	encrypted, err := secure.Parse(repo.Keys.Private, repo.Hash, string(raw))
-	if err != nil {
-		log.Errorf("failure to decrypt secure parameters for %s. %s", repo.FullName, err)
-	}
-	if encrypted != nil && len(encrypted) != 0 {
-		raw = []byte(inject.InjectSafe(string(raw), encrypted))
-	}
-
 	c.JSON(202, build)
 
 	queue_.Publish(&queue.Work{
-		User:  user,
-		Repo:  repo,
-		Build: build,
-		Keys:  repo.Keys,
-		Netrc: netrc,
-		Yaml:  raw,
+		User:   user,
+		Repo:   repo,
+		Build:  build,
+		Keys:   repo.Keys,
+		Netrc:  netrc,
+		Config: raw,
+		Secret: sec,
 		System: &common.System{
 			Link:    httputil.GetURL(c.Request),
 			Plugins: conf.Plugins,
diff --git a/pkg/server/hooks.go b/pkg/server/hooks.go
index 70b34d6ff..b66004efb 100644
--- a/pkg/server/hooks.go
+++ b/pkg/server/hooks.go
@@ -10,9 +10,7 @@ import (
 	common "github.com/drone/drone/pkg/types"
 	"github.com/drone/drone/pkg/utils/httputil"
 	"github.com/drone/drone/pkg/yaml"
-	"github.com/drone/drone/pkg/yaml/inject"
 	"github.com/drone/drone/pkg/yaml/matrix"
-	"github.com/drone/drone/pkg/yaml/secure"
 )
 
 // PostHook accepts a post-commit hook and parses the payload
@@ -93,25 +91,13 @@ func PostHook(c *gin.Context) {
 	build.RepoID = repo.ID
 
 	// fetch the .drone.yml file from the database
-	raw, err := remote.Script(user, repo, build)
+	raw, sec, err := remote.Script(user, repo, build)
 	if err != nil {
 		log.Errorf("failure to get .drone.yml for %s. %s", repo.FullName, err)
 		c.Fail(404, err)
 		return
 	}
-	// inject any private parameters into the .drone.yml
-	if repo.Params != nil && len(repo.Params) != 0 {
-		raw = []byte(inject.InjectSafe(string(raw), repo.Params))
-	}
-	encrypted, err := secure.Parse(repo.Keys.Private, repo.Hash, string(raw))
-	if err != nil {
-		log.Errorf("failure to decrypt secure parameters for %s. %s", repo.FullName, err)
-		c.Fail(400, err)
-		return
-	}
-	if encrypted != nil && len(encrypted) != 0 {
-		raw = []byte(inject.InjectSafe(string(raw), encrypted))
-	}
+
 	axes, err := matrix.Parse(string(raw))
 	if err != nil {
 		log.Errorf("failure to calculate matrix for %s. %s", repo.FullName, err)
@@ -160,12 +146,13 @@ func PostHook(c *gin.Context) {
 	}
 
 	queue_.Publish(&queue.Work{
-		User:  user,
-		Repo:  repo,
-		Build: build,
-		Keys:  repo.Keys,
-		Netrc: netrc,
-		Yaml:  raw,
+		User:   user,
+		Repo:   repo,
+		Build:  build,
+		Keys:   repo.Keys,
+		Netrc:  netrc,
+		Config: raw,
+		Secret: sec,
 		System: &common.System{
 			Link:    httputil.GetURL(c.Request),
 			Plugins: conf.Plugins,
diff --git a/pkg/server/repos.go b/pkg/server/repos.go
index 09933faaa..951639d4a 100644
--- a/pkg/server/repos.go
+++ b/pkg/server/repos.go
@@ -1,8 +1,8 @@
 package server
 
 import (
-	"encoding/json"
 	"fmt"
+	"io/ioutil"
 
 	"github.com/drone/drone/Godeps/_workspace/src/github.com/gin-gonic/gin"
 	"github.com/drone/drone/Godeps/_workspace/src/github.com/gin-gonic/gin/binding"
@@ -249,16 +249,17 @@ func PostRepo(c *gin.Context) {
 //
 func Encrypt(c *gin.Context) {
 	repo := ToRepo(c)
-
-	in := map[string]string{}
-	json.NewDecoder(c.Request.Body).Decode(&in)
-	privKey := sshutil.UnMarshalPrivateKey([]byte(repo.Keys.Private))
-	err := secure.EncryptMap(secure.ToHash(repo.Hash), &privKey.PublicKey, in)
+	in, err := ioutil.ReadAll(c.Request.Body)
 	if err != nil {
 		c.Fail(500, err)
 		return
 	}
-	c.JSON(200, &in)
+	out, err := secure.Encrypt(string(in), repo.Keys.Private)
+	if err != nil {
+		c.Fail(500, err)
+		return
+	}
+	c.Writer.Write([]byte(out))
 }
 
 // Unsubscribe accapets a request to unsubscribe the
diff --git a/pkg/yaml/secure/secure.go b/pkg/yaml/secure/secure.go
index 09e282644..36f88fe9e 100644
--- a/pkg/yaml/secure/secure.go
+++ b/pkg/yaml/secure/secure.go
@@ -2,71 +2,45 @@ package secure
 
 import (
 	"crypto/rsa"
-	"crypto/sha256"
-	"hash"
+	"crypto/x509"
+	"encoding/pem"
 
-	"github.com/drone/drone/Godeps/_workspace/src/gopkg.in/yaml.v2"
-
-	"github.com/drone/drone/pkg/utils/sshutil"
+	"github.com/square/go-jose"
 )
 
-// Parse parses and returns the secure section of the
-// yaml file as plaintext parameters.
-func Parse(privateKeyPEM, repoHash, raw string) (map[string]string, error) {
-	params, err := parseSecure(raw)
+// Encrypt encrypts a secret string.
+func Encrypt(in, privKey string) (string, error) {
+	rsaPrivKey, err := decodePrivateKey(privKey)
 	if err != nil {
-		return nil, err
+		return "", err
 	}
 
-	hasher := ToHash(repoHash)
-	privKey := sshutil.UnMarshalPrivateKey([]byte(privateKeyPEM))
-
-	err = DecryptMap(hasher, privKey, params)
-	return params, err
+	return encrypt(in, &rsaPrivKey.PublicKey)
 }
 
-// DecryptMap decrypts values of a map of named parameters
-// from base64 to decrypted strings.
-func DecryptMap(hasher hash.Hash, privKey *rsa.PrivateKey, params map[string]string) error {
-	var err error
+// decodePrivateKey is a helper function that unmarshals a PEM
+// bytes to an RSA Private Key
+func decodePrivateKey(privateKey string) (*rsa.PrivateKey, error) {
+	derBlock, _ := pem.Decode([]byte(privateKey))
+	return x509.ParsePKCS1PrivateKey(derBlock.Bytes)
+}
 
-	for name, encrypted := range params {
-		params[name], err = sshutil.Decrypt(hasher, privKey, encrypted)
-		if err != nil {
-			return err
-		}
+// encrypt encrypts a plaintext variable using JOSE with
+// RSA_OAEP and A128GCM algorithms.
+func encrypt(text string, pubKey *rsa.PublicKey) (string, error) {
+	var encrypted string
+	var plaintext = []byte(text)
+
+	// Creates a new encrypter using defaults
+	encrypter, err := jose.NewEncrypter(jose.RSA_OAEP, jose.A128GCM, pubKey)
+	if err != nil {
+		return encrypted, err
 	}
-	return nil
-}
-
-// EncryptMap encrypts values of a map of named parameters
-func EncryptMap(hasher hash.Hash, pubKey *rsa.PublicKey, params map[string]string) error {
-	var err error
-
-	for name, value := range params {
-		params[name], err = sshutil.Encrypt(hasher, pubKey, value)
-		if err != nil {
-			return err
-		}
+	// Encrypts the plaintext value and serializes
+	// as a JOSE string.
+	object, err := encrypter.Encrypt(plaintext)
+	if err != nil {
+		return encrypted, err
 	}
-	return nil
-}
-
-// parseSecure is helper function to parse the Secure data from
-// the raw yaml file.
-func parseSecure(raw string) (map[string]string, error) {
-	data := struct {
-		Secure map[string]string
-	}{}
-	err := yaml.Unmarshal([]byte(raw), &data)
-
-	return data.Secure, err
-}
-
-// ToHash is helper function to generate Hash of given string
-func ToHash(key string) hash.Hash {
-	hasher := sha256.New()
-	hasher.Write([]byte(key))
-	hasher.Reset()
-	return hasher
+	return object.CompactSerialize()
 }