Between 1999 and 2005, 233 stranded cetaceans (comprising 19 species) were reported in the waters of the Canary Islands. Of these, 138/233 (59.2%) were subjected to a complete or partial standardized necropsy, including 4 Balaenopteridae, 9 Physeteridae, 8 Kogiidae, 27 Ziphiidae and 90 Delphinidae. Of these, 46/138 (33.3%) cetaceans were diagnosed with anthropogenic pathological categories (i.e. the cause of death was anthropogenic). These included fishing interaction (bycatch) (19 individuals), 'atypical' mass stranding events linked to naval exercises (13), ship collisions (8) and other anthropogenic-related pathology (6). 'Natural' (i.e. non-anthropogenic) causes of death accounted for another 82/138 (59.4%) cases, including infectious and non-infectious diseases (63), neonatal pathology (8), intra- and interspecific interactions (6) and mass strandings (5). The cause(s) of death could not be determined in 10/138 (7.3%) necropsied animals. The most common causes of death were ship collisions in 6/9 (66.6%) Physeteridae, 'atypical' mass stranding linked to naval exercises in 13/27 (48.1%) Ziphiidae, and 'natural' infectious and non-infectious diseases in 55/90 (61.1%) Delphinidae. Interaction with fishing activities was established as cause of death in 15/90 (16.7%) Delphinidae. These data show that a range of anthropogenic and natural single and mass mortality events occur in multiple cetacean species stranded in the Canary Islands.