Look at it this way...

If you take the second story of a 2 story house and set it next to the first story...

1. You lose one insulated exterior wall...a savings.

2. You practically double the amount of foundation required...a cost.

3. You practically double the amount of roof required...a cost.

4. You eliminate stairs to the second floor...a savings.

5. Assuming all other things in the house are the same...number of rooms, baths, etc., flooring, interior walls (although an increase in bearing walls required), plumbing, wiring, etc., it's probably slightly more expensive to build the same square footage as a single story.

But then again, it depends on where you live, cost of materials, cost of labor (how hungry the builders are for work), and a few code issues.

per square foot it is cheaper for two floor home. Here in nyc concrete is expensive. a yard can be $75. Labor, excavating,drainage expensive. Compared to building a wooden deck for the second story per square foot a second story makes sense.