Aims:  To examine the virulence factors and the genetic relationship isolates of the serogroup O3 of Vibrio parahaemolyticus in outbreaks of diarrhoea in the northeast region of Brazil. Methods and Results:  Eighteen samples of the O3:K6 and O3:KUT serotypes of V. parahaemolyticus were analysed by multiplex polymerase chain reaction (m‐PCR) for detection of the tl, tdh and trh genes, by random‐amplified polymorphic DNA (RAPD) using two primers, and by amplification of the rDNA 16S–23S region. The gene tl was amplified in all the samples, tdh in 16 while trh in none; amplification of rDNA 16S–23S generated only one profile; each RAPD primer produced two amplification patterns allowing grouping two tdh– Kanagawa‐negative isolates. Conclusions:  V. parahaemolyticus with characteristics of the pandemic clone appears to be widely disseminated in the studied region. Because of the genetic uniformity of the isolates, elucidation of outbreaks or tracking the source of contamination by the present molecular techniques seems useless. Significance and Impact of the Study:  Detection of V. parahaemolyticus with virulence potential of pandemic clone from two outbreaks and from several isolated gastroenteritis cases points out the need for inclusion of this micro‐organism in the Brazilian routine monitoring of the diarrhoeas for elucidation of their aetiology.