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is driving on the freeway with your sunroof open just as bad as driving with your windows down in terms of gas mileage?  

i think that depends of you're creating drag or not.i think some sunroofs have sort of an "air dam" or whatever it's called that will deflect the air to keep it all from rushing in and creating drag.  i think generally the aerodynamics of most cars keep air from going into the sunroof at high speeds anyway...i could be wrong though.  

I think the effect of your sunroof will really depend on the specific car. My first reaction would be that it isn't as big of effect since it is a smaller opening and a large portion of the air flow spills off the side of the car instead of going over it. However having your sunroof open could really effect the amount of parasitic drag behind the car. Interesting question with too may variables to just guess at.  

To answer the question, think about how turbulent your car feels inside with the windows down vs the sunroof.  In my car its relatively calm with the sunroof, but thundering loud with the windows down.  I would say that you DO cause some drag with the sunroof but not as much as with your windows open.  As far as parasitic drag behind the car I have no idea.