Between September 1990 and December 2002, 511 cetacean carcasses stranded or caught in commercial fisheries in England and Wales were examined post mortem. Salmonella group B was isolated from 60 of 279 (21.51%) harbour porpoises (Phocoena phocoena), predominantly from lung tissue. Forty-three of the Salmonella group B isolates were subsequently serotyped and all found to have the antigenic structure O4,12:a:-. The annual proportion of harbour porpoises testing positive for Salmonella O4,12:a:- increased significantly from 6% in the early 1990s to 27% after 1999. The cause(s) of the increasing prevalence of Salmonella O4,12:a:- are not known, but may reflect natural variation in the epidemiological cycle of Salmonella O4,12:a:- in harbour porpoises. The probability of isolating Salmonella O4,12:a:- from harbour porpoises increased with age, suggesting that the mode of transmission is principally horizontal. There appeared to be a weak degree of seasonality in the probability of isolating Salmonella O4,12:a:- with a low proportion of cases in the months of April and May. Based on pathological findings from infected carcasses, Salmonella O4,12:a:- may be part of the normal commensal flora of the lungs of cetaceans with the potential to act as an opportunistic pathogen.