We report three cases of congenital malaria involving two malarial immune mothers living in Spain. Diagnostic PCR and Genotyping PCR for merozoite surface proteins 1 and 2 were essential to show that mothers and new-borns had different Plasmodium population parasites at the moment of the delivery, and that the infection was acquired earlier in gestation by transplacental transmission. In the first case the Plasmodium species founded in both, mother and child were different. Malaria in the twins showed a mixed infection (P. falciparum plus P. malariae) while the mother presented a P. falciparum infection. These facts were confirmed studying the polymorphisms for MSP1 and MSP2. Blood samples of the newborns were analyzed an half hour after delivery excluding the possibility of re-infection by mosquito bite and indicating a vertical transmission during pregnancy.