Abstract Cytogenetic biomarkers are essential for assessing environmental exposure that can predict adverse human health effects such as cellular damage. Chromosomal aberrations are the most important cytogenetic end-points successfully used for the cancer risk assessment of populations occupationally or environmentally exposed to different toxic chemicals. Previous reports suggest that, increased frequency of chromosomal aberration (CA), in peripheral blood lymphocytes, is a predictor of cancer. Arsenic is a paradoxical human carcinogen, clastogen and aneugen. Despite of exposure at similar extent, only 15–20% of individuals show arsenic induced skin lesions including Bowen's disease (BD). Previously we have reported the significant increase in CA in the individuals with arsenic induced skin lesions when compared to individuals without any skin lesions, drinking arsenic contaminated water at similar extent. Presently, a matched case-control study was performed to examine whether biomarkers such as chromosomal aberrations can predict the development of arsenic induced Bowen's (in situ carcinoma) diseases. Chromosomal aberrations (both chromosome and chromatid types) and mitotic index were analyzed from the lymphocytes of 25 cases of Bowen's patient which was compared to matched control from the individuals with arsenic induced non-cancerous skin lesions such as raindrop pigmentation, keratosis of palm and sole, hypo and hyper pigmentation. Chromosomal aberrations/cell, chromosome type aberrations and total percentage of aberrant cells were significantly higher in cases compared to control ( p < 0.01). These results suggest that chromosomal aberrations can be used for cancer risk assessment of the population exposed to arsenic through drinking water.