Malaria has always been a major cause of death in the tropics, and antimalarial drugs have played a key role in controlling its spread through the treatment of patients infected with plasmodial parasites and the control of its transmissibility. On the other hand, antimalarial drugs may exert adverse effects and side-effects that can sometimes be serious. Atovaquone (ATO) and proguanil hydrochloride (PROG) is the fixed combination for the prevention and treatment of Plasmodium falciparum malaria. As safe and effective antimalarial drugs are needed in both the treatment and the prophylaxis of malaria, this study was performed in order to investigate their possible cytogenotoxic potential towards human lymphocytes, as non-target cells, and the possible mechanism responsible for it. Two different concentrations of ATO and PROG, either alone or in combination, were used with and without S9 fraction. The concentrations used were those found in human plasma when a fixed-dose combination of ATO and PROG was used: 2950/130 ng/mL after prophylactic treatment and 11800/520 ng/mL after treatment of malaria, respectively. Possible cellular and DNA-damaging effects were evaluated by cell viability and alkaline comet assays, while oxidative stress potential was evaluated by formamidopyrimidine-DNA glycosylase (Fpg)-modified comet assay, in addition to assessing malondialdehyde and glutathione levels as biomarkers of oxidative stress. Based on the obtained results, single exposure to ATO did not display cytogenotoxic effect while PROG showed week but significant cytogenotoxic potential. The ATO/PROG combination also displayed weak but significant cytogenotoxic potential towards human lymphocytes with no impact on oxidative stress parameters, suggesting that oxidative stress is not implicated in their mechanism of action. Given that the key portion of the damaging effects was induced after S9 metabolic activation, it is to presume that the principal metabolite of PROG, cycloguanil, had the greatest impact on their cytogenotoxic potential. The obtained results indicate that the ATO/PROG combination is relatively safe for the consumption from the aspect of cytogenotoxicity, especially if used for prophylaxis. Nevertheless, further cytogenetic research and regular patient monitoring are warranted to minimize the risk of adverse events especially among frequent travellers.