The diagnosis of Leishmania (Leishmania) infantum infection in children from birth may serve as a reference for the early identification of cases that would progress to classical visceral leishmaniasis (VL) in endemic areas. This study prospectively evaluated newborns of mothers living in the municipality of Paracatu, Minas Gerais, Brazil. The infants were followed up at 6-month intervals by clinical examination, serological tests (immunofluorescence [IIF] and enzyme-linked immunosorbent assay with rK39 [ELISA-rK39]) and polymerase chain reaction (PCR) until they had completed 18 months of age. A total of 166 pregnant women were included to evaluate the possible transfer of antibodies or even congenital transmission. Twenty-two of the women tested positive by IIF, four by ELISA-rK39, and one by PCR. Three infants of the 25 women with some positive test results were also positive in the first test (one by IIF, one by ELISA-rK39, and the third by ELISA-rK39 and PCR). One hundred and sixty infants were included in the study; of these, 43 had at least one positive sample over time. However, agreement between tests was low. Follow-up of children with a positive result in the tests studied revealed no progression to classical disease within a period of 18 months. In contrast, two children with negative IIF, PCR, and ELISA-rK39 results developed classical VL at 9 and 12 months of age. In conclusion, a positive test result was variable and sometimes temporary and agreement between tests was low. Therefore, the early diagnosis of Leishmania infection was not associated with the early identification of cases that would progress to classical VL in the endemic area studied.