Colony-forming eutrophic marine microorganisms in ballast water were counted in samples taken on board in 2002 and 2003. In the ballast water in Japan, viable cell numbers were highly variable but not by more than 10(5.1) colony-forming units (CFU)ml(-1) regardless of season. Even when ballast water was discharged offshore, values varied but not by more than 10(5.0) CFUml(-1). The effectiveness of the ballast water exchange was unconfirmed, except for the February 2003 voyage. No microbial colonies were counted in the reloaded ballast water in the high seas on that voyage, which contributed to the reduction of the total number of viable cells sampled in the discharged ballast water at the Ras Laffan port in Qatar. In sediment samples, the values of 10(5.2) - 10(6.0) CFUml(-1) were estimated for all seasons in which voyages took place. The maximum of the marine Vibrio species, 110 CFUml(-1), was observed in the ballast water sample taken in July 2003. The estimated total viable cell numbers in sediments were higher than those counted in the ballast water throughout the experiments, indicating the importance of sediment management as well as ballast water management on vessels traveling from Japan.