Mercury-contaminated effluent was discharged into Minamata Bay from a chemical plant over a period of approximately 40 years until 1968. In October 1977, the Minamata Bay Pollution Prevention Project was initiated to dispose of sedimentary sludge containing mercury concentrations higher than 25 mg kg(-1). In March 1990, the project was completed. In an effort to estimate current contamination in the bay, the vertical and horizontal distributions of mercury in sediment were investigated. Sediment core samples were collected on June 26, 2002 at 16 locations in Minamata Bay and Fukuro Bay located in the southern part of Minamata Bay. The sediment in Fukuro Bay had not been dredged. The total mercury concentration in surface sediment was 1.4-4.3 mg kg(-1) (2.9+/-0.9 mg kg(-1), n=9) for the dredged area of Minamata Bay and 0.3-4.8 mg kg(-1) (3.6+/-1.6 mg kg(-1), n=4) for Fukuro Bay. In the lower layers of long cores taken from both areas, the total mercury concentration decreased with depth and finally showed relatively uniform low values. These values can be considered to represent the background concentration absent of anthropogenic influence, which was estimated for the study area to be 0.068+/-0.012 mg kg(-1) (n=10). From the surface, the total mercury concentration in Fukuro Bay increased with depth and reached a maximum at 8-14 cm. In Minamata Bay, several centimeters from the surface the total mercury concentration did not change significantly having considerably higher values than the background level. At six stations, the methylmercury concentration was determined. Although the vertical variations were similar to those for total mercury, Fukuro Bay sediment showed a higher concentration of methylmercury than Minamata Bay sediment.