DNA damage plays a crucial role in the transforming potential of the human carcinogen arsenic. The arsenic biotransformation enzyme AS3MT is known to participate in the generation of ROS after arsenic exposure, whereas MTH1 sanitizes oxidized dNTP pools to prevent the incorporation of damaged bases into DNA. In this work, we sought to assess the role of these two enzymes in the genotoxic and carcinogenic effects of arsenic exposure. Thus, mouse embryonic fibroblasts (MEF), transformed by chronic arsenite exposure, were monitored for DNA damage by the comet and the micronucleus assays at different time-of-exposure intervals lasting for 50 weeks. Results indicate that the oxidative and DNA damage of chronically exposed MEF cells increased time-dependently up to the point of transformation. As3mt expression followed a pattern like that of DNA damage, and its forced inhibition by shRNA technology before transformation resulted in a DNA damage decrease. On the other hand, Mth1 mRNA levels increased after the transformation point, and its forced knock-down increased significantly the levels of DNA damage and decreased the aggressiveness of the oncogenic phenotype. Thus, As3mt and Mth1 have important differential roles in the accumulation of DNA damage linked to the transformation process: while As3mt contributes to the genotoxic effects before the transformation, Mth1 prevents the DNA damage fixation after the acquisition of the oncogenic phenotype. This study demonstrates the influence of As3mt and Mth1 in arsenic DNA damage induction and it is the first to present Mth1 as a candidate modulator biomarker of the tumoral phenotype.