Yes, it's something you have to careful with! - normally an opamp will use a split supply (say + and - 12V), in this case you would normally measure with respect to the 0V point (the junction of the two supplies), and would get positive and negative voltages.
If the opamp is fed from a single supply, you may well measure from the -ve rail - in which case you would only get positive voltages.
As I said, you need to be careful, and aware of where you measure from!.