Interpretation of the possible effects of pollution on the health of marine animals requires baseline information from reference populations in clean environments. This paper reviews literature on the natural diseases and infections of large whales with an emphasis on two filter-feeding species inhabiting the central North Atlantic (fin whale, Balaenoptera physalus, and sei whale, B. borealis). Despite evidence that the abundance of North Atlantic fin and sei whales is now depressed as a result of commercial exploitation, both suffer from serious endemic infections with incidences exceeding 90 percent. Pathological and biochemical findings lead to a conclusion that in severe infections the principal nematode parasite of the fin whale probably can kill its host. Recognizing a positive relationship between population density and exposure to endemic pathogens, it is cautioned that pollution-driven mortality events in expanding marine populations could be mimicked, masked, or amplified by natural phenomena.