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Caffeine is a widely consumed substance, and there is a discussion about its effects when ingested by women during pregnancy and lactation. We aimed to identify the genotoxic effects of caffeine in female mice that consumed it during pregnancy and lactation periods and its consequences in their offspring. Thirty-six couples of Swiss mice received water or caffeine (0.3 and 1.0 mg/mL) treatment during pregnancy and lactation. The male and female offspring were divided into 12 groups according to the treatment administered to the female mice. Genotoxicity was assessed using the comet assay and the micronucleus test. Both doses of caffeine showed genotoxic effects in pregnant and lactating mice groups compared to groups not administered caffeine. In relation to offspring, it can be observed that females and males of the offspring had low weight in early life. In both female and male offspring, genotoxicity was detected in the blood, liver, and kidney tissues. Thus, from the present study, we can suggest that the caffeine consumed by female mice during the periods of pregnancy and lactation led to genotoxic effects in their offspring.