Background: Congenital malaria is defined as malarial parasites demonstrated in the peripheral blood smear of the newborn from twenty four hours to seven days of life. Malaria is endemic in India, neonatal disease is considered rare. Routine screening for malaria is essential for all neonates with fever in endemic areas. Early diagnosis and treatment of malaria could effectively prevent infant mortality. The aim of the present observational prospective study is to describe the occurrence and clinical spectrum of congenital vivax malaria in admitted neonates in Bikaner, India (low endemic region). Congenital malaria has been predominantly reported for P. falciparum from different parts of the world but the reports with P. vivax are very scanty. Methods: This prospective study was conducted on admitted neonate from January 2011 to December 2012. The species diagnosis was done by peripheral blood smear examination and rapid diagnostic test. The possibilities of other disease/infections causing similar illness were investigated thoroughly and stringently. A structured questionnaire was used to collect clinical data on newborn and maternal health during pregnancy. Results: A total of 1168 new born admitted in first week of life were screened. Out of them 23 (1.97%) had evidence of parasitaemia ( P. vivax 17 and P. falciparum 6). The criteria for admission in these 17 neonates with congenital vivax malaria were LBW and prematurity (41.18%), septicemia (35.29%), perinatal asphyxia (17.65%), jaundice (17.65%) and seizures (5.88%). Conclusions: This study emphasizes the occurrence of P. vivax congenital malaria even in neonates in low transmission area and without typical manifestations. The emphasis is also on the relevance even in very low transmission areas of not only maintaining, but even increasing clinical and epidemiological awareness of this preventable and treatable disease in pregnancy and in the neonate.