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Background: Limited evidence exists on perinatal transmission and outcomes of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in neonates. Objective: To describe clinical outcomes and risk factors for transmission in neonates born to mothers with perinatal SARS-CoV-2 infection. Design: Prospective cohort of suspected and confirmed SARS-CoV-2 infected neonates entered in National Neonatology Forum (NNF) of India registry. Subjects: Neonates born to women with SARS-CoV-2 infection within two weeks before or two days after birth and neonates with SARS-CoV-2 infection. Outcomes: Incidence and risk factors of perinatal transmission. Results: Among 1713 neonates, SARS-CoV-2 infection status was available for 1330 intramural and 104 extramural neonates. SARS-CoV-2 positivity was reported in 144 intramural and 39 extramural neonates. Perinatal transmission occurred in 106 (8%) and horizontal transmission in 21 (1.5%) intramural neonates. Neonates roomed-in with mother had higher transmission risk (RR1.16, 95% CI 1.1 to 2.4; P=0.01). No association was noted with the mode of delivery or type of feeding. The majority of neonates positive for SARS-CoV2 were asymptomatic. Intramural SARS-CoV-2 positive neonates were more likely to be symptomatic (RR 5, 95%CI 3.3 to 7.7; P<0.0001) and need resuscitation (RR 2, 95%CI 1.0 to 3.9; P=0.05) compared to SARS-CoV-2 negative neonates. Amongst symptomatic neonates, most morbidities were related to prematurity and perinatal events. Conclusion: Data from a large cohort suggests perinatal transmission of SARS-CoV-2 infection and increased morbidity in infected infants. [ABSTRACT FROM AUTHOR]