Evaluation of the presence of genotoxic substances is especially important in rivers that serve as a source of drinking water. Nine water samples collected along the river Rasina in Serbia were analyzed for potential toxic and genotoxic effects using the Allium anaphase-telophase test. Inhibition of root growth relative to the negative control (synthetic water) was observed in all samples. Analysis of the genotoxic potential, through scoring anaphase and telophase aberrations, showed that in seven of the nine samples the level of aberrations was significantly increased relative to the negative control but was lower than that obtained for the positive control (methyl methanesulfonate). Changes in the relation between spindle and chromosome types of aberrations were found in some samples, indicating differences in the potential genotoxic substances present at the analyzed sites. The data, which were obtained from samples collected at the highest level of river water, warn that during periods of low flow the values could reach genotoxic activity. The Allium anaphase-telophase test can be recommended as an monitoring system, that can serve as the first alert for the presence of genotoxic environmental pollutants.