Fisheries bycatch is considered to be one of the most significant causes of mortality for many marine species, including vulnerable megafauna. In the open ocean, tuna purse seiners are known to use several cetacean species to detect tuna schools. This exposes the cetaceans to encirclement which can lead to incidental injury or death. While interactions between fishers and cetaceans have been well documented in the eastern tropical Pacific Ocean, little is known about these interactions and potential mortalities in the tropical Atlantic and Indian Oceans. Here, we provide the first quantification of these interactions in both oceans by analyzing a large database of captain’s logbooks (1980 to 2011) and observations collected by onboard scientific observers (1995 to 2011). Distribution maps of sightings per unit effort highlighted main areas of relatively high co-occurrence: east of the Seychelles (December to March), the Mozambique Channel (April to May) and the offshore waters of Gabon (April to September). The percentage of cetacean-associated fishing sets was around 3% in both oceans and datasets whereas 0.6% of sets had cetaceans encircled. Of the 194 cetaceans encircled in a purse seine net (122 baleen whales, 72 delphinids), immediate apparent survival rates were high (Atlantic: 92%, Indian: 100%). Among recorded mortalities, 8 involved pantropical spotted dolphins Stenella attenuata and 3 involved humpback whales Megaptera novaeangliae. These high survival rates suggest that setting nets close to cetaceans has a low immediate apparent impact on the species involved. Our findings will contribute to the development of an ecosystem approach to managing fisheries and accurate cetacean conservation measures.