Microcystins (MCs) are the toxic products of harmful algal blooms and they accumulate in fish. The accumulation of MCs in fish living in different trophic levels from different parts of Lake Taihu was determined. This information was then used to evaluate the risks posed by the MCs in fish to human health. The concentrations of three MCs, MC-LR, MC-YR and MC-RR, were quantified in the following four fish species: silver carp (Hypophthalmichthys molitrix), bighead carp (Aristichthys nobilis), crucian carp (Carassius auratus) and common carp (Cyprinus carpio), using high performance liquid chromatography interfaced with tandem (triple quadrupole) mass spectrometry. The mean concentrations of MCs in the muscle, the kidney, the intestinal wall and the heart were significantly different among the four fishes except in the liver. C. carpio contained the highest mean concentration of MCs in the muscle (31.7 ± 12.1 ng/g, dry mass (dm)), whereas C. auratus had the highest mean concentrations of MCs in the liver (45.4 ± 44.5 ng/g, dm), kidney (114 ± 51.1 ng/g, dm), intestinal wall (2.04 × 10 3 ± 4.43 × 10 3 ng/g, dm) and heart (59.5 ± 26.7 ng/g, dm). The mean concentration of MCs in the intestinal walls of the fish species was significantly higher than in other organs (p b 0.01). The fish from Meiliang Bay had significantly higher concentrations of MCs than those from the centre, west or south banks of the lake (p b 0.01). The body lengths and masses of the fish were negatively correlated with the concentrations of MCs in the kidney (p b 0.05) and heart (p b 0.01). The average daily intake (ADI) of MCs in the muscle of all fishes exceeded the provisional tolerable daily intake (TDI) set by World Health Organization. The estimated daily intakes of MCs in 55.6% of the muscle samples exceeded the TDI. The MCs in the tissues of the fish from Lake Taihu pose potential risks to the health of humans who consume these four fish species.