Is there any risk of illness from eating store-bought salsa?

Yes, but it isn't likely. Because of the way some salsa ingredients are farmed, harvested, and processed, salsa may be contaminated with E. coli O157:H7, salmonella, and Listeria  monocytogenes. These ingredients that may be contaminated include tomatoes, onions, and peppers. However, the FDA mandates that all salsas be pasteurized either immediately before or after packaging. The most common pasteurization method is heat, which effectively kills food-borne pathogens. In fact, many salsas are heated to higher than normal temperatures to extend shelf life (the amount of time the salsa will keep). 
 
Once opened, salsa is subject to mold growth and spoilage.  Fortunately, proper storage and  handling eliminates most risk of illness.
 
Source(s):
Food Engineering Magazine "An Extended Romance: Minimally Processed Foods"