I lived on Long Island for 2009. However at the end of my state return, turbo tax says I owe approximately $2,500 for a city of New York resident tax. Why is this? I did not live within the 5 boroughs during 2009.

You're correct - only NYC residents pay NYC resident tax, so if you did live in the 5 boroughs you do not pay it. Go back and check what you entered for personal information in the program. Perhaps you entered a mailing address that's in the city?

Thanks for the response...

I think it is just another glitch with Turbo Tax for New York State. I've had several issues with it already. I recently bought a home in February that I am applying for the first time home buyer tax credit. Even though I clicked on the button that says it was NOT my address for 2009, Turbro Tax seems to have an issue distinguishing between the two different addresses.