Babesiosis is a tick-borne disease with an increasing number of cases each year. Due to the non-specific symptoms of babesiosis, insightful analyses of the pathogenesis of babesiosis are still very important. Transmission of the disease occurs in a few ways, which makes laboratory diagnosis of piroplasmosis important. Complications associated with the infection can be tragic, especially in patients with immunological disorders. The aim of this study was the histopathological analysis of the spleen and kidney of young Wistar rats infected transplacentally with Babesia microti. Female rats were infected with a reference strain of B. microti (ATCC 30221), and then, birth 3-week-old males were euthanized with isoflurane. Subsequently, the material was collected at autopsy for microscopic and ultrastructural examination. Microscopic and ultrastructural analysis of the spleen and kidney showed degenerative changes within the organ parenchyma and the capsules surrounding the organ. Regenerative and reparative changes through mitotic divisions of parenchymal cells were also evident. Merozoites of B. microti were visible in the section of erythrocytes and the cells building the organ stroma. The results presented in this study proved the negative effects of B. microti on cells and tissues in rats with congenital babesiosis.