diff --git a/app.js b/app.js
index 73ea810..6b73b51 100644
--- a/app.js
+++ b/app.js
@@ -99,14 +99,15 @@ app.use(bodyParser.json());
 
 
 
-/* Middlewares */
+/* Includes */
+
+// Middlewares
+require('./core/middlewares/loader').process(app, global.opts);
 
 // Auth initializing
 var auth = require('./core/auth')(app);
 app.use(auth.everyauth.middleware());
 
-// Clarify
-app.use(require('./core/middleware/clarify'));
 
 // File tree module
 var fileTree = require('./core/file-tree');
@@ -135,29 +136,6 @@ app.use('/api/updateFileTree', function(req, res){
 });
 
 
-// Middleware that loads spec content
-var read = require("./core/middleware/read");
-app.use(read.process);
-
-// Markdown
-app.use(require("./core/middleware/md").process);
-app.use(require("./core/middleware/mdTag").process);
-
-// Load user defined middleware, that processes spec content
-require("./core/middleware/userMiddleware");
-
-// Middleware that wraps spec with Source template
-app.use(require("./core/middleware/wrap").process);
-
-// Middleware that sends final spec response
-app.use(require("./core/middleware/send").process);
-
-/* /Middlewares */
-
-
-
-/* Includes */
-
 // Routes
 require('./core/routes');
 
@@ -233,7 +211,7 @@ app.use(logErrors);
 
 
 
-// Server start
+/* Server start */
 if (!module.parent) {
     var serverOpts = global.opts.core.server;
     var port = serverOpts.port;
@@ -256,3 +234,4 @@ if (!module.parent) {
             });
     }
 }
+/* Server start */
diff --git a/core/middleware/userMiddleware.js b/core/middleware/userMiddleware.js
deleted file mode 100644
index b09952f..0000000
--- a/core/middleware/userMiddleware.js
+++ /dev/null
@@ -1,26 +0,0 @@
-'use strict';
-
-/**
- *
- * Loading user middleware
- *
- * */
-
-var fs = require('fs');
-var path = require('path');
-var pathToUserMiddleware = path.join(global.app.get('user'), 'node_modules');
-
-// Loading all sourcejs-*/core/index.js files from npm plugins section
-if (fs.existsSync(pathToUserMiddleware)) {
-    var userMiddlewareFiles = fs.readdirSync(pathToUserMiddleware);
-
-    userMiddlewareFiles.map(function (file) {
-        if ((/^sourcejs-/).test(file)) {
-            var pluginIndexPath = path.join(pathToUserMiddleware, file, 'core/middleware', 'index.js');
-            if (fs.existsSync(pluginIndexPath)) {
-                var middleware = require(pluginIndexPath);
-                global.app.use(middleware.process);
-            }
-        }
-    });
-}
\ No newline at end of file
diff --git a/core/middleware/clarify.js b/core/middlewares/clarify.js
similarity index 99%
rename from core/middleware/clarify.js
rename to core/middlewares/clarify.js
index caea523..cae0b58 100644
--- a/core/middleware/clarify.js
+++ b/core/middlewares/clarify.js
@@ -229,7 +229,7 @@ var getSectionsIDList = function(sections) {
     return output;
 };
 
-module.exports = function(req, res, next) {
+module.exports.process = function(req, res, next) {
 	var parsedUrl = url.parse(req.url, true);
 
     // Query params
diff --git a/core/middlewares/loader.js b/core/middlewares/loader.js
new file mode 100644
index 0000000..35de9e7
--- /dev/null
+++ b/core/middlewares/loader.js
@@ -0,0 +1,162 @@
+'use strict';
+
+var _ = require('lodash');
+var fs = require('fs');
+var path = require('path');
+
+var appRoot = path.resolve('./');
+var utils = require(path.join(appRoot, 'core/lib/utils'));
+var log = require(path.join(appRoot, 'core/logger')).log;
+
+var gatherMiddlewares = function(dest, filterRegExp, mainJS){
+    var output = {};
+
+    if (fs.existsSync(dest)) {
+        var userMiddlewareFiles = fs.readdirSync(dest);
+
+        userMiddlewareFiles.map(function (dir) {
+            if (!filterRegExp || filterRegExp.test(dir)) {
+                var middlewareName = dir;
+                var _mainJS = mainJS || 'index.js';
+
+                var pluginIndexPath = path.join(dest, dir, _mainJS);
+                if (fs.existsSync(pluginIndexPath)) {
+                    output[middlewareName] = {
+                        enabled: true,
+                        order: 0,
+                        group: 'default',
+                        indexPath: pluginIndexPath
+                    };
+
+                    // Load middleware options
+                    var configPath = path.join(dest, dir, 'options.js');
+                    if (fs.existsSync(configPath)) {
+                        var middlewareConfig = require(configPath);
+
+                        _.forOwn(output[middlewareName], function (value, key) {
+                            var overVal = middlewareConfig[key];
+
+                            if (overVal) {
+                                if (key === 'order') {
+                                    if (overVal >= 0) {
+                                        output[middlewareName][key] = overVal;
+                                    } else {
+                                        log.warn('Middlewares are restricted to define order with value lower than 0 (zero). Please modify '+ middlewareName+ ' middleware options.');
+                                    }
+                                } else {
+                                    output[middlewareName][key] = overVal;
+                                }
+                            }
+                        });
+                    }
+                }
+            }
+        });
+    }
+
+    return output;
+};
+
+var sortMiddlewares = function(groupsOrder, list){
+    var output = [];
+
+    if (!(groupsOrder && _.isArray(groupsOrder) && list)) return output;
+
+    var groupedList = {};
+
+    // Sort by groups
+    _.forOwn(list, function (value, key) {
+        var group = value.group || 'default';
+        var middleware = value;
+
+        if (!middleware.enabled) return;
+
+        middleware.name = middleware.name || key;
+
+        groupedList[group] = groupedList[group] || [];
+        groupedList[group].push(value);
+    });
+
+    // Sort each group
+    _.forOwn(groupedList, function (value, key) {
+        groupedList[key] = _.sortByOrder(value, ['order'], ['asc']);
+    });
+
+    // Concat groups by order
+    groupsOrder.forEach(function(item){
+        if (groupedList[item]) output = output.concat(groupedList[item]);
+    });
+
+    return output;
+};
+
+var loadMiddlewares = function(listArr, app){
+    if (!_.isArray(listArr) && !app) return;
+
+    log.debug('loading', listArr);
+
+    listArr.forEach(function(item){
+        if (item && item.indexPath && fs.existsSync(item.indexPath)) {
+            app.use(require(item.indexPath).process);
+        }
+    });
+};
+
+module.exports.process = function(app, globalOptions){
+    var config = {
+        loadGroupsOrder: [
+            'request',
+            'pre-html',
+            'default',
+            'html',
+            'response'
+        ],
+        list: {
+            md: {
+                enabled: true,
+                order: -1,
+                group: 'pre-html',
+                indexPath: path.join(appRoot, 'core/middlewares/md.js')
+            },
+            mdTag: {
+                enabled: true,
+                order: 0,
+                group: 'html',
+                indexPath: path.join(appRoot, 'core/middlewares/mdTag.js')
+            },
+            clarify: {
+                enabled: true,
+                order: -2,
+                group: 'request',
+                indexPath: path.join(appRoot, 'core/middlewares/clarify.js')
+            },
+            read: {
+                enabled: true,
+                order: -1,
+                group: 'request',
+                indexPath: path.join(appRoot, 'core/middlewares/read.js')
+            },
+            send: {
+                enabled: true,
+                order: -1,
+                group: 'response',
+                indexPath: path.join(appRoot, 'core/middlewares/send.js')
+            },
+            wrap: {
+                enabled: true,
+                order: -1,
+                group: 'html',
+                indexPath: path.join(appRoot, 'core/middlewares/wrap.js')
+            }
+        }
+    };
+    utils.extendOptions(
+        config,
+        {
+            list: gatherMiddlewares(path.join(app.get('user'), 'node_modules'), new RegExp(/^sourcejs-/), 'core/middleware/index.js')
+        },
+        globalOptions.core.middlewares
+    );
+
+    loadMiddlewares(sortMiddlewares(config.loadGroupsOrder, config.list), app);
+};
\ No newline at end of file
diff --git a/core/middleware/md.js b/core/middlewares/md.js
similarity index 95%
rename from core/middleware/md.js
rename to core/middlewares/md.js
index 9653b0b..971aa41 100644
--- a/core/middleware/md.js
+++ b/core/middlewares/md.js
@@ -21,6 +21,8 @@ exports.process = function (req, res, next) {
         var end = process.hrtime(start);
         global.log.debug('Markdown processing took: ', prettyHrtime(end));
 
+        req.specData.isMd = false;
+
         next();
     } else {
         next();
diff --git a/core/middleware/mdTag.js b/core/middlewares/mdTag.js
similarity index 100%
rename from core/middleware/mdTag.js
rename to core/middlewares/mdTag.js
diff --git a/core/middleware/read.js b/core/middlewares/read.js
similarity index 100%
rename from core/middleware/read.js
rename to core/middlewares/read.js
diff --git a/core/middleware/send.js b/core/middlewares/send.js
similarity index 100%
rename from core/middleware/send.js
rename to core/middlewares/send.js
diff --git a/core/middleware/wrap.js b/core/middlewares/wrap.js
similarity index 100%
rename from core/middleware/wrap.js
rename to core/middlewares/wrap.js