I think it depends on the school and on your situation and also what was covered in the class.
When I took general microbiology, I was told by the professor and (indirectly) by some admissions people that it should count. However, this seemed to be because it was a general micro course, rather than one with a specific focus (medical micro, for example? I'm not sure I fully understand this part), so I would definitely discuss the course with someone familiar with it and pre-med requirements.
(caveat: I had placed out of the one semester of intro to life science my school offered as general bio. This might have influenced things, also. Further, I am a junior, while I did get the input of a few admissions people on my situation, I have obviously not applied to medical school yet.)