In order to study the pollution with microcystin (MC), a potent liver promoter, in drinking water in highly endemic area of liver cancer, cyanobacteria and its product MC were detected in drinking water in Haimen, Jiangsu Province during 1992 to 1993. Oscillatoria was identified as the most common species of cyanobacteria in pond-ditch and river water in Haimen, Jiangsu Province, which can produce MC. MC was detected in two of 65 water samples with high performance liquid chromatography, liquid chromatography and mass spectrography. In addition, studies were conducted in 989 samples collected from drinking water in Haimen, Jiangsu Province and more sensitive ELISA was used to detect their MC contents. Results showed proportions of samples with positive MC (greater than 50 pg/ml) were 17.3%, 31.9%, 4.3% and 0 for pond-ditch, river, shallow and deep well water, respectively, with average contents of 101, 160, 68 and 0 pg/ml, respectively. Proportions of positive MC samples and average MC contents for pond-ditch water were significantly greater than those in shallow and deep well water. It suggests studies on relationship between MC and liver cancer should be conducted further.