The river Nile is the main source of drinking water in Egypt. Nutrient loading coupled with year-round warm weather favor the growth of cyanobacteria, several of which can produce cyanotoxins, especially the potent liver toxins called microcystins. Most microcystin resides inside or closely attached to cyanobacteria cells, and are released into the water column as cells lyse from senescence or chemical treatment. The present study evaluated microcystin levels, as measured by immunoassay (ELISA), in both raw and finished drinking water of the river Nile, during the warm season (May-October), near the drinking water intake for Sohag City, Egypt. The results showed that microcystin content within the cells correlated better with type of microcystin-producing cyanobacteria (Gomphosphaeria, Microcystis, Oscillatoria) rather than chlorophyll a. Microcystin concentration in cell-free water correlated significantly with that measured within the cells, with maximum values being recorded in September (0.4-0.78 µg l-1). Microcystin levels in the finished drinking water were low (56.1- 87.1 ng l-1) and were detected only in May and June. The study indicates that microcystin is present in the raw and finished drinking water at Sohag City but that levels did not exceed the World Health Organization (WHO) drinking water guideline level of 1µg l-1 during May-October 1999.