We developed an anti-immune complex (IC) ELISA applicable to direct determination of trace amounts of microcystins (MCs) in tap water. Comparison of two assay formats revealed that the use of anti-immune complex monoclonal antibody (MAB) in the coating step to trap anti-MC MAB–MC complexes improved the sensitivity as well as precision. The detection limit and quantitative range of the IC ELISA was 2 pg ml−1and 2–100 pg ml−1of microcystinLR (MCLR), respectively, indicating the most sensitive of all the methods for detecting MCs reported to date. Additionally, the IC ELISA maintained good reliability through its quantitative range, as evidenced by low coefficients of variation (5.0–10.8 and 4.9–10.2% for intra- and interassay, respectively). The IC ELISA showed good cross-reactivity to microcystin-RR and microcystin-YR, suggesting major MCs found in the environment can be detected by this method. Recovery tests in which quantitative range of MCLR were added to tap water resulted in a mean recovery of 99%, with a mean standard deviation of 5.7%; therefore the IC ELISA performed well in the analysis of tap water samples. ELISA analysis of tap water samples collected in China and Japan revealed that, among 17 samples tested, two samples collected in China were positive for MCs at 4.9–14 pg ml−1. These results suggest that the newly developed IC ELISA can be used to monitor trace amounts of MCs in tap water.