diff --git a/index.js b/index.js
index 9dafccc21..532f88c3d 100644
--- a/index.js
+++ b/index.js
@@ -1,12 +1,11 @@
 'use strict';
 
 var sort = require('./lib/sort'),
-  concat = require('concat-stream'),
   nestParams = require('./lib/nest_params'),
   filterAccess = require('./lib/filter_access'),
   filterJS = require('./lib/filter_js'),
-  dependency = require('./streams/input/dependency'),
-  shallow = require('./streams/input/shallow'),
+  dependency = require('./lib/input/dependency'),
+  shallow = require('./lib/input/shallow'),
   parse = require('./lib/parsers/javascript'),
   polyglot = require('./lib/parsers/polyglot'),
   github = require('./lib/github'),
@@ -47,11 +46,12 @@ module.exports = function (indexes, options, callback) {
     indexes = [indexes];
   }
 
-  var inputStream = options.polyglot ?
-    shallow(indexes).pipe(polyglot()) :
-    (options.shallow ? shallow(indexes) : dependency(indexes, options));
+  var inputFn = (options.polyglot || options.shallow) ? shallow : dependency;
 
-  return inputStream.pipe(concat(function (inputs) {
+  return inputFn(indexes, options, function (error, inputs) {
+    if (error) {
+      return callback(error);
+    }
     try {
       var flat = inputs
         .filter(filterJS)
@@ -77,7 +77,7 @@ module.exports = function (indexes, options, callback) {
     } catch (e) {
       callback(e);
     }
-  }));
+  });
 };
 
 module.exports.formats = {
diff --git a/streams/input/dependency.js b/lib/input/dependency.js
similarity index 56%
rename from streams/input/dependency.js
rename to lib/input/dependency.js
index 2254696e6..4ddae9133 100644
--- a/streams/input/dependency.js
+++ b/lib/input/dependency.js
@@ -1,7 +1,10 @@
 'use strict';
 
 var mdeps = require('module-deps'),
+  fs = require('fs'),
   path = require('path'),
+  babelify = require('babelify'),
+  concat = require('concat-stream'),
   moduleFilters = require('../../lib/module_filters');
 
 /**
@@ -13,22 +16,33 @@ var mdeps = require('module-deps'),
  *
  * @param {Array<string>} indexes paths to entry files as strings
  * @param {Object} options optional options passed
- * @param {Array<Object>} [options.transform=[]] optional array of transforms
- * @returns {ReadableStream} output
+ * @param {Function} callback called with (err, inputs)
+ * @returns {undefined} calls callback
  */
-function dependencyStream(indexes, options) {
+function dependencyStream(indexes, options, callback) {
   var md = mdeps({
     filter: function (id) {
       return !!options.external || moduleFilters.internalOnly(id);
     },
-    transform: options.transform,
+    transform: [babelify.configure({
+      sourceMap: false
+    })],
     postFilter: moduleFilters.externals(indexes, options)
   });
   indexes.forEach(function (index) {
     md.write(path.resolve(index));
   });
   md.end();
-  return md;
+  md.once('error', function (error) {
+    return callback(error);
+  });
+  md.pipe(concat(function (inputs) {
+    callback(null, inputs.map(function (input) {
+      // un-transform babelify transformed source
+      input.source = fs.readFileSync(input.file, 'utf8');
+      return input
+    }));
+  }));
 }
 
 module.exports = dependencyStream;
diff --git a/streams/input/shallow.js b/lib/input/shallow.js
similarity index 75%
rename from streams/input/shallow.js
rename to lib/input/shallow.js
index b55c6dbf2..446050c64 100644
--- a/streams/input/shallow.js
+++ b/lib/input/shallow.js
@@ -1,6 +1,5 @@
 'use strict';
 
-var streamify = require('stream-array');
 var fs = require('fs');
 
 /**
@@ -16,10 +15,12 @@ var fs = require('fs');
  * or without fs access.
  *
  * @param {Array<string|Object>} indexes entry points
- * @return {ReadableStream} this emits data
+ * @param {Object} options parsing options
+ * @param {Function} callback called with (err, inputs)
+ * @return {undefined} calls callback
  */
-module.exports = function (indexes) {
-  return streamify(indexes.map(function (index) {
+module.exports = function (indexes, options, callback) {
+  return callback(null, indexes.map(function (index) {
     if (typeof index === 'string') {
       return {
         source: fs.readFileSync(index, 'utf8'),
diff --git a/lib/parsers/javascript.js b/lib/parsers/javascript.js
index 66d0f9e6b..1ae03d10e 100644
--- a/lib/parsers/javascript.js
+++ b/lib/parsers/javascript.js
@@ -34,7 +34,6 @@ var parseOpts = {
   }
 };
 
-
 /**
  * Receives a module-dep item,
  * reads the file, parses the JavaScript, and parses the JSDoc.
diff --git a/package.json b/package.json
index ed215b274..b950281ab 100644
--- a/package.json
+++ b/package.json
@@ -16,6 +16,7 @@
   },
   "dependencies": {
     "ast-types": "^0.8.12",
+    "babelify": "^6.3.0",
     "babylon": "^5.8.23",
     "brfs": "^1.4.0",
     "concat-stream": "^1.5.0",
diff --git a/test/fixture/bad/syntax.output.json b/test/fixture/bad/syntax.output.json
index d9965a79f..5d6b9f535 100644
--- a/test/fixture/bad/syntax.output.json
+++ b/test/fixture/bad/syntax.output.json
@@ -3,5 +3,7 @@
   "loc": {
     "line": 1,
     "column": 0
-  }
+  },
+  "_babel": true,
+  "codeFrame": "> 1 | *\n    | ^\n  2 | "
 }
\ No newline at end of file
diff --git a/test/fixture/jsx.input.js b/test/fixture/jsx.input.js
new file mode 100644
index 000000000..f8d352467
--- /dev/null
+++ b/test/fixture/jsx.input.js
@@ -0,0 +1,7 @@
+var util = require('util');
+
+/**
+ * This function returns the number one.
+ * @returns {Number} numberone
+ */
+module.exports = (<p>hello</p>);
diff --git a/test/fixture/jsx.output.custom.md b/test/fixture/jsx.output.custom.md
new file mode 100644
index 000000000..5eb617f6e
--- /dev/null
+++ b/test/fixture/jsx.output.custom.md
@@ -0,0 +1,9 @@
+# exports
+
+This function returns the number one.
+
+
+Returns **Number** numberone
+
+
+
diff --git a/test/fixture/jsx.output.json b/test/fixture/jsx.output.json
new file mode 100644
index 000000000..4f7c22f5e
--- /dev/null
+++ b/test/fixture/jsx.output.json
@@ -0,0 +1,64 @@
+[
+  {
+    "description": "This function returns the number one.",
+    "tags": [
+      {
+        "title": "returns",
+        "description": "numberone",
+        "lineNumber": 2,
+        "type": {
+          "type": "NameExpression",
+          "name": "Number"
+        }
+      }
+    ],
+    "loc": {
+      "start": {
+        "line": 3,
+        "column": 0
+      },
+      "end": {
+        "line": 6,
+        "column": 3
+      }
+    },
+    "context": {
+      "loc": {
+        "start": {
+          "line": 7,
+          "column": 0
+        },
+        "end": {
+          "line": 7,
+          "column": 32
+        }
+      },
+      "code": "var util = require('util');\n\n/**\n * This function returns the number one.\n * @returns {Number} numberone\n */\nmodule.exports = (<p>hello</p>);\n"
+    },
+    "errors": [
+      "memberof reference to module not found"
+    ],
+    "returns": [
+      {
+        "title": "returns",
+        "description": "numberone",
+        "lineNumber": 2,
+        "type": {
+          "type": "NameExpression",
+          "name": "Number"
+        }
+      }
+    ],
+    "name": "exports",
+    "memberof": "module",
+    "scope": "static",
+    "members": {
+      "instance": [],
+      "static": []
+    },
+    "events": [],
+    "path": [
+      "exports"
+    ]
+  }
+]
\ No newline at end of file
diff --git a/test/fixture/jsx.output.md b/test/fixture/jsx.output.md
new file mode 100644
index 000000000..5eb617f6e
--- /dev/null
+++ b/test/fixture/jsx.output.md
@@ -0,0 +1,9 @@
+# exports
+
+This function returns the number one.
+
+
+Returns **Number** numberone
+
+
+
diff --git a/test/fixture/jsx.output.md.json b/test/fixture/jsx.output.md.json
new file mode 100644
index 000000000..a563ea3d5
--- /dev/null
+++ b/test/fixture/jsx.output.md.json
@@ -0,0 +1,139 @@
+{
+  "type": "root",
+  "children": [
+    {
+      "type": "root",
+      "children": [
+        {
+          "depth": 1,
+          "type": "heading",
+          "children": [
+            {
+              "type": "text",
+              "value": "exports"
+            }
+          ]
+        },
+        {
+          "type": "root",
+          "children": [
+            {
+              "type": "paragraph",
+              "children": [
+                {
+                  "type": "text",
+                  "value": "This function returns the number one.",
+                  "position": {
+                    "start": {
+                      "line": 1,
+                      "column": 1
+                    },
+                    "end": {
+                      "line": 1,
+                      "column": 38
+                    },
+                    "indent": []
+                  }
+                }
+              ],
+              "position": {
+                "start": {
+                  "line": 1,
+                  "column": 1
+                },
+                "end": {
+                  "line": 1,
+                  "column": 38
+                },
+                "indent": []
+              }
+            }
+          ],
+          "position": {
+            "start": {
+              "line": 1,
+              "column": 1
+            },
+            "end": {
+              "line": 1,
+              "column": 38
+            }
+          }
+        },
+        {
+          "type": "root",
+          "children": [
+            {
+              "type": "paragraph",
+              "children": [
+                {
+                  "type": "text",
+                  "value": "Returns "
+                },
+                {
+                  "type": "strong",
+                  "children": [
+                    {
+                      "type": "text",
+                      "value": "Number"
+                    }
+                  ]
+                },
+                {
+                  "type": "text",
+                  "value": " "
+                },
+                {
+                  "type": "root",
+                  "children": [
+                    {
+                      "type": "paragraph",
+                      "children": [
+                        {
+                          "type": "text",
+                          "value": "numberone",
+                          "position": {
+                            "start": {
+                              "line": 1,
+                              "column": 1
+                            },
+                            "end": {
+                              "line": 1,
+                              "column": 10
+                            },
+                            "indent": []
+                          }
+                        }
+                      ],
+                      "position": {
+                        "start": {
+                          "line": 1,
+                          "column": 1
+                        },
+                        "end": {
+                          "line": 1,
+                          "column": 10
+                        },
+                        "indent": []
+                      }
+                    }
+                  ],
+                  "position": {
+                    "start": {
+                      "line": 1,
+                      "column": 1
+                    },
+                    "end": {
+                      "line": 1,
+                      "column": 10
+                    }
+                  }
+                }
+              ]
+            }
+          ]
+        }
+      ]
+    }
+  ]
+}
\ No newline at end of file
diff --git a/test/streams/input/shallow.js b/test/lib/input/shallow.js
similarity index 66%
rename from test/streams/input/shallow.js
rename to test/lib/input/shallow.js
index 81b0784e4..7a5f92482 100644
--- a/test/streams/input/shallow.js
+++ b/test/lib/input/shallow.js
@@ -1,28 +1,28 @@
 'use strict';
 
 var test = require('tap').test,
-  concat = require('concat-stream'),
   path = require('path'),
-  shallow = require('../../../streams/input/shallow');
+  shallow = require('../../../lib/input/shallow');
 
 test('shallow deps', function (t) {
-  shallow([path.resolve(path.join(__dirname, '../../fixture/es6.input.js'))])
-    .pipe(concat(function (deps) {
-      t.equal(deps.length, 1);
-      t.ok(deps[0].file, 'has file');
-      t.end();
-    }));
+  shallow([path.resolve(path.join(__dirname, '../../fixture/es6.input.js'))], {}, function (err, deps) {
+    t.ifError(err);
+    t.equal(deps.length, 1);
+    t.ok(deps[0].file, 'has file');
+    t.end();
+  });
 });
 
 test('shallow deps multi', function (t) {
   shallow([
     path.resolve(path.join(__dirname, '../../fixture/es6.input.js')),
     path.resolve(path.join(__dirname, '../../fixture/es6.output.json'))
-  ]).pipe(concat(function (deps) {
+  ], {}, function (err, deps) {
+    t.ifError(err);
     t.equal(deps.length, 2);
     t.ok(deps[0].file, 'has file');
     t.end();
-  }));
+  });
 });
 
 test('shallow deps literal', function (t) {
@@ -32,8 +32,9 @@ test('shallow deps literal', function (t) {
   };
   shallow([
     obj
-  ]).pipe(concat(function (deps) {
+  ], {}, function (err, deps) {
+    t.ifError(err);
     t.equal(deps[0], obj);
     t.end();
-  }));
+  });
 });
diff --git a/test/test.js b/test/test.js
index a49f1d0db..9311bcb67 100644
--- a/test/test.js
+++ b/test/test.js
@@ -90,11 +90,13 @@ test('bad input', function (tt) {
         t.equal(res, undefined);
         // make error a serializable object
         error = JSON.parse(JSON.stringify(error));
+        // remove system-specific path
+        delete error.filename;
         var outputfile = file.replace('.input.js', '.output.json');
         if (UPDATE) {
           fs.writeFileSync(outputfile, JSON.stringify(error, null, 2));
         }
-        var expect = require(outputfile);
+        var expect = JSON.parse(fs.readFileSync(outputfile));
         t.deepEqual(error, expect);
         t.end();
       });