diff --git a/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp b/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp
index c0314dd89caf..641f10315eb5 100644
--- a/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp
+++ b/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp
@@ -14702,18 +14702,18 @@ void ApplicationWindow::parseCommandLineArguments(const QStringList& args)
     return;
   }
 
+  bool exec(false), quit(false), default_settings(false),
+       unknown_opt_found(false);
+  QString file_name;
   QString str;
-  bool exec = false;
-  bool quit = false;
-  bool default_settings = false;
+  int filename_argindex, counter(0);
   foreach(str, args) {
     if( (str == "-v" || str == "--version") ||
         (str == "-r" || str == "--revision") ||
         (str == "-a" || str == "--about") ||
         (str == "-h" || str == "--help") )
     {
-      QMessageBox::critical(this, tr("MantidPlot - Error"),//Mantid
-          tr("<b> %1 </b>: This command line option must be used without other arguments!").arg(str));
+      g_log.warning() << str.ascii() << ": This command line option must be used without other arguments!";
     }
     else if( (str == "-d" || str == "--default-settings"))
     {
@@ -14728,24 +14728,36 @@ void ApplicationWindow::parseCommandLineArguments(const QStringList& args)
     {
       exec = true;
       quit = true;
-      // Minimize ourselves
-      this->showMinimized();
     }
-    else if (str.startsWith("-") || str.startsWith("--"))
+    // if filename not found yet then these are all program arguments so we should
+    // know what they all are
+    else if (file_name.isEmpty() && (str.startsWith("-") || str.startsWith("--")))
     {
-      QMessageBox::critical(this, tr("MantidPlot - Error"),//Mantid
-          tr("<b> %1 </b> unknown command line option!").arg(str) + "\n" + tr("Type %1 to see the list of the valid options.").arg("'MantidPlot -h'"));
+      g_log.warning() << "'" << str.ascii() << "' unknown command line option!\n"
+                      << "Type 'MantidPlot -h'' to see the list of the valid options.";
+      unknown_opt_found = true;
+      break;
+    }
+    else
+    {
+      // First option that doesn't start "-" is considered a filename and the rest arguments to that file
+      if(file_name.isEmpty())
+      {
+        file_name = str;
+        filename_argindex = counter;
+      }
     }
+    ++counter;
   }
 
-  QString file_name = args[num_args-1]; // last argument
-  if(file_name.startsWith("-")){// no file name given
+  if(unknown_opt_found || file_name.isEmpty())
+  {// no file name given
     initWindow();
     savedProject();
     return;
   }
-
-  if (!file_name.isEmpty()){
+  else
+  {
     QFileInfo fi(file_name);
     if (fi.isDir()){
       QMessageBox::critical(this, tr("MantidPlot - Error opening file"),//Mantid
@@ -14764,10 +14776,17 @@ void ApplicationWindow::parseCommandLineArguments(const QStringList& args)
     workingDir = fi.dirPath(true);
     saveSettings();//the recent projects must be saved
 
+    QStringList cmdArgs = args;
+    cmdArgs.erase(cmdArgs.begin(), cmdArgs.begin() + filename_argindex);
+    // Set as arguments in script environment
+    scriptingEnv()->setSysArgs(cmdArgs);
+
     if (exec)
     {
       if(quit)
       {
+        // Minimize ourselves
+        this->showMinimized();
         try
         {
           executeScriptFile(file_name, Script::Asynchronous);
@@ -16450,7 +16469,7 @@ ApplicationWindow * ApplicationWindow::loadScript(const QString& fn, bool existi
  *  Runs a script from a file. Mainly useful for automatically running scripts
  * @param filename The full path to the file
  * @param execMode How should the script be executed. If asynchronous
- * this method waits on the thread finishing
+ *                 this method waits on the thread finishing
  */
 void ApplicationWindow::executeScriptFile(const QString & filename, const Script::ExecutionMode execMode)
 {
diff --git a/Code/Mantid/MantidPlot/src/PythonScripting.cpp b/Code/Mantid/MantidPlot/src/PythonScripting.cpp
index fddb9b776ba3..7bc26a1e4ce1 100644
--- a/Code/Mantid/MantidPlot/src/PythonScripting.cpp
+++ b/Code/Mantid/MantidPlot/src/PythonScripting.cpp
@@ -90,6 +90,20 @@ PythonScripting::~PythonScripting()
 {
 }
 
+/**
+ * @param args A list of strings that denoting command line arguments
+ */
+void PythonScripting::setSysArgs(const QStringList &args)
+{
+  GlobalInterpreterLock gil;
+
+  PyObject *argv = toPyList(args);
+  if(argv && m_sys)
+  {
+    PyDict_SetItemString(m_sys, "argv", argv);
+  }
+}
+
 /**
  * Create a new script object that can execute code within this environment
  *
@@ -271,13 +285,31 @@ QStringList PythonScripting::toStringList(PyObject *py_seq)
       PyObject *item = PyList_GetItem(py_seq, i);
       if( PyString_Check(item) )
       {
-  elements << PyString_AsString(item);
+        elements << PyString_AsString(item);
       }
     }
   }
   return elements;
 }
 
+/**
+ * Returns a new Python list from the given Qt QStringList
+ * @param items A reference to a QStringList object
+ * @return A new reference to a Python list. Caller is responsible for calling Py_DECREF
+ */
+PyObject *PythonScripting::toPyList(const QStringList &items)
+{
+  Py_ssize_t length = static_cast<Py_ssize_t>(items.length());
+  PyObject * pylist = PyList_New((length));
+  for(Py_ssize_t i = 0; i < length; ++i)
+  {
+    QString item = items.at(static_cast<int>(i));
+    PyList_SetItem(pylist, i,
+                   PyString_FromString(item.ascii()));
+  }
+  return pylist;
+}
+
 /**
  * Returns an integer representation of the object as a c long. No check is performed to see if it is an integer
  * @param object :: A PyInt_Type instance
diff --git a/Code/Mantid/MantidPlot/src/PythonScripting.h b/Code/Mantid/MantidPlot/src/PythonScripting.h
index bdc25d11a087..bddc4d55bc19 100644
--- a/Code/Mantid/MantidPlot/src/PythonScripting.h
+++ b/Code/Mantid/MantidPlot/src/PythonScripting.h
@@ -57,6 +57,9 @@ class PythonScripting: public ScriptingEnv
   /// 'Fake' method needed for IPython import
   void set_parent(PyObject*) {}
 
+  /// Set the argv attribute on the sys module
+  void setSysArgs(const QStringList & args);
+
   /// Create a new script object that can execute code within this enviroment
   virtual Script *newScript(const QString &name, QObject * context, const Script::InteractionType interact) const;
 
@@ -69,8 +72,10 @@ class PythonScripting: public ScriptingEnv
 
   /// Return a string represenation of the given object
   QString toString(PyObject *object, bool decref = false);
-  //Convert a Python list object to a Qt QStringList
+  /// Convert a Python list object to a Qt QStringList
   QStringList toStringList(PyObject *py_seq);
+  /// Convert a QtringList to a Python List
+  PyObject * toPyList(const QStringList & items);
   /// Returns an integer representation of the object. No check is performed to see if it is an integer
   long toLong(PyObject *object, bool decref = false);
 
diff --git a/Code/Mantid/MantidPlot/src/ScriptingEnv.h b/Code/Mantid/MantidPlot/src/ScriptingEnv.h
index fd72eb046e74..9499be40f0d9 100644
--- a/Code/Mantid/MantidPlot/src/ScriptingEnv.h
+++ b/Code/Mantid/MantidPlot/src/ScriptingEnv.h
@@ -63,8 +63,9 @@ class ScriptingEnv : public QObject
 
   /// Is the environment initialized
   bool isInitialized() const { return d_initialized; }
-  /// Query if any code is currently being executed
-  //bool isRunning() const { return m_is_running; }
+
+  /// If the environment supports it, set the system arguments
+  virtual void setSysArgs(const QStringList & args) = 0;
 
   /// Create a script object that is responsible for executing actual code
   virtual Script *newScript(const QString &name, QObject * context, const Script::InteractionType interact) const = 0;
@@ -76,7 +77,7 @@ class ScriptingEnv : public QObject
   /// Return a documentation string for the given mathematical function.
   virtual const QString mathFunctionDoc(const QString&) const { return QString::null; }
   /// Return a list of file extensions commonly used for this language.
-  virtual const QStringList fileExtensions() const { return QStringList(); };
+  virtual const QStringList fileExtensions() const { return QStringList(); }
   /// Construct a filter expression from fileExtension(), suitable for QFileDialog.
   const QString fileFilter() const;
   /// Return the name of the scripting language supported by this environment
diff --git a/Code/Mantid/MantidPlot/src/muParserScripting.cpp b/Code/Mantid/MantidPlot/src/muParserScripting.cpp
index 44394330aee6..fcf2b9e60e0e 100644
--- a/Code/Mantid/MantidPlot/src/muParserScripting.cpp
+++ b/Code/Mantid/MantidPlot/src/muParserScripting.cpp
@@ -89,6 +89,11 @@ const muParserScripting::mathFunction muParserScripting::math_functions[] = {
   {0,0,NULL,NULL,NULL,0}
 };
 
+void muParserScripting::setSysArgs(const QStringList &)
+{
+  throw std::runtime_error("muParserScripting does not support command line arguments");
+}
+
 const QStringList muParserScripting::mathFunctions() const
 {
   QStringList l;
diff --git a/Code/Mantid/MantidPlot/src/muParserScripting.h b/Code/Mantid/MantidPlot/src/muParserScripting.h
index 38615e3ff36f..ac4440c86fab 100644
--- a/Code/Mantid/MantidPlot/src/muParserScripting.h
+++ b/Code/Mantid/MantidPlot/src/muParserScripting.h
@@ -52,10 +52,13 @@ class muParserScripting: public ScriptingEnv
     muParserScripting(ApplicationWindow *parent) : ScriptingEnv(parent, langName) { d_initialized=true; }
     static ScriptingEnv *constructor(ApplicationWindow *parent) { return new muParserScripting(parent); }
 
-  Script *newScript(const QString &name, QObject * context, const Script::InteractionType) const
-  {
-    return new muParserScript(const_cast<muParserScripting*>(this), name, context);
-  }
+    /// Set the system arguments. Throws an exception as it is not supported
+    void setSysArgs(const QStringList & args);
+
+    Script *newScript(const QString &name, QObject * context, const Script::InteractionType) const
+    {
+      return new muParserScript(const_cast<muParserScripting*>(this), name, context);
+    }
     
     virtual bool supportsEvaluation() { return true; }