Chikungunya is an arboviral disease transmitted by Aedes species mosquito. As per systematic reviews, vertical transmission is seen in upto 50 % cases. Congenital infection in neonates present with predominant central nervous system involvement, characteristic cutaneous hyperpigmentation and thrombocytopenia. We are presenting here two cases. First baby presented with fever and hyperpigmentation while other neonate had encephalopathy followed by facial hyperpigmentation. Maternal chikungunya IgM antibody titres were positive and baby’s blood RT-PCR for chikungunya virus were also positive in both the cases .A strong clinical suspicion should be kept when a newborn presents with features of encephalopathy, perioral hyperpigmentation, especially in endemic areas, where mother is suffering from viral fever with or without rash in the peripartum period.