Definitely a red flag. Try to get to the bottom of it - some of the best opportunities can look like this one. But understanding why it has been vacant for 12 years is the key here. Plus, using the building for a different purpose can be interesting. I would proceed with caution, ask around - neighbors, city officials, etc.
@Richard S. : Clearly there has not been any demand for the price. You are asking the correct question... why? Something has to be different for it to be worth it.
A few things... is it available for rent or for sale? If for rent... was the price too high? Is the market in the area changing? Meaning... is there big development occurring or a major corporation moving in? Did a Starbucks open up nearby? If the area is stagnant, it probably is not worth it.
There is always the concern of non-use. For example, is the plumbing still good?
You could try to put an option contract on it. Then market the space and see if any bites that make the price you want to pay workable.
If not then throw it back and do not buy it.