BackgroundBabesia microti is an emerging tick-borne pathogen and the causative agent of human babesiosis. Mathematical modeling of the reproductive rate of B. microti indicates that it cannot persist in nature by horizontal tick-host transmission alone. We hypothesized that transplacental transmission in the reservoir population contributes to B. microti persistence and emergence in North American rodent populations.MethodsPeromyscus leucopus were collected from Connecticut and Block Island, Rhode Island and analyzed using a highly specific quantitative PCR (qPCR) assay for infection with B. microti.ResultsIn April, 100% (n = 103) of mice were infected with B. microti. Females exhibited significantly higher parasitemia than their offspring (P < 0.0001) and transplacental transmission was observed in 74.2% of embryos (n = 89). Transplacental transmission of B. microti is thus a viable and potentially important infectious pathway in naturally infected rodent species and should be considered in future theoretical and empirical studies.ConclusionsTo our knowledge, this study is the first to report transplacental transmission of B. microti occurring in its natural reservoir host, P. leucopus, in the United States and the only study that provides a quantitative estimate of parasitemia. This vector-independent pathway could contribute to the increased geographic range of B. microti or increase its abundance in endemic areas.Electronic supplementary materialThe online version of this article (10.1186/s13071-018-2875-8) contains supplementary material, which is available to authorized users.