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You can change the font used for input and output cells in all notebooks to your preferred one, such as Courier, by evaluating the following:

    CurrentValue[$FrontEnd, {StyleHints, "CodeFont"}] = "Courier"    

This will undo these changes.

   CurrentValue[$FrontEnd, {StyleHints, "CodeFont"}] = Inherited     

Note that the fonts used in mathematics typesetting are the supplied MathFonts. This setting cannot be changed.

To alter the styling of a given font, edit the input or output cell style in a stylesheet.

Here we demonstrate the procedure for input cells. The procedure for output cells is the same.

1. From the menu bar, select Format ► Edit Stylesheet. A blank stylesheet opens.
2. Under Customize Inherited Style, select the Input cell style and make sure the Input cell bracket is highlighted.
   

   
   
   

3. Use the Format menu selection to edit the characteristics (Format ► Face or Background Color, for example). Here we change the font face to italic:
   

   
   

4. Click the File ► Install... An install dialog appears. Enter the stylesheet name and select who the users will be. Click OK to confirm.
   
   

Now this stylesheet is available under Format ► Stylesheet.

You may wish to make this stylesheet the default one for your Mathematica.