Abstract Interactions between cetaceans and the purse-seine fishery operating along the whole Portuguese continental coast were studied based on on-board observations from 2010 to 2011. Cetacean presence and mortality were estimated and characteristics under which interactions were most likely to occur were identified. Observations were made on 163 fishing trips (0.7% of the average annual number of fishing trips) and 302 fishing operations/hauls. Cetaceans were present during 16.9% of fishing events; common dolphins (Delphinus delphis) accounted for 96% of occurrences, mostly overnight in summer and early autumn. Regression models showed that cetacean presence during a fishing set was significantly (p < 0.05) associated with sardine catches, effort, and latitude/longitude. Encirclement and mortality occurred in 2.3 and 1.0% of fishing events, respectively. Encircled species were the common dolphin, bottlenose dolphin (Tursiops truncatus), and harbour porpoise (Phocoena phocoena), but only common dolphin showed mortality (three individuals); raised to fleet level, estimated total mortality rates of common dolphins were 69 (95% CI 37–110) in the north and 91 (95% CI 55–165) in the south for 2010 and 78 (95% CI 47–140) in the south only for 2011. The estimated annual mortality rate due to purse seining is 113 (95% CI 3–264) common dolphins, which is ∼0.63% of the current most optimistic estimate of population size for the Portuguese fishing area (SCANS II). The wide confidence limits, as well as variation between years, reflect low observer coverage, emphasizing the need for increased monitoring to cover gaps in the spatial and seasonal distribution of observer effort and provide reliable estimates of bycatch.