When chlorine is used as a disinfectant for drinking water it may react with organic materials present in or released by the water pipes and thus form by-products that may represent a genotoxic hazard. The aim of this study was to assess the potential genotoxicity and cytotoxicity of extracts of chlorinated drinking water supplied by local aquifers of two Italian towns, Plants 1 and 2, located in the sub-Alpine area and on the Po plain, respectively. The raw water fell within the legal limits with regards to its chemical and physical properties. Water from Plant 2 contained higher levels of total organics (TOC) and nitrate than water from Plant 1. Water was sampled at different points along the distribution networks to evaluate the influence of the system on the amount and quality of the by-products. Cytotoxic and genotoxic damage was assessed in freshly isolated human white blood cells (WBC) and Hep-G2 cells by use of the micronucleus (MN) test and the Comet assay to measure primary DNA damage. While they did not show significant cytotoxicity, all Plant 1 water concentrates induced short-time genotoxic effects on leukocytes at concentrations ≥1Lequiv./mL. Plant 2 samples were able to induce cytotoxic effects in both Hep-G2 cells and leukocytes. Furthermore, although there was no significant increase in MN frequency, DNA migration was strongly increased both in human leukocytes (≥0.5Lequiv./mL, 1h treatment, water samples collected from all points) and in Hep-G2 cells (≥0.75Lequiv./mL, 24h treatment, tap water sampled at the nearest distribution point). The current use of these in vitro cytotoxicity/genotoxicity tests together with the normal chemical analyses could provide information to help water-works managers and health authorities evaluate drinking water quality and adopt strategies to reduce genotoxic compounds in tap water and prevent human exposure to these compounds.