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ObjectiveTo examine infants in Scotland aged 0-27 days with confirmed SARS-CoV-2 infection; the risk of neonatal infection by factors including maternal infection status and gestation at birth; and the need for hospital admission among infected neonates. DesignPopulation-based cohort study. Setting and populationAll live births in Scotland, 1 March 2020 to 31 January 2022. ResultsThere were 141 neonates with confirmed SARS-CoV-2 infection over the study period, giving an overall infection rate of 153 per 100,000 live births (141/92,009). Among infants born to women with confirmed infection around the time of birth, the infection rate was 1,811 per 100,000 live births (15/828). Nearly two-thirds (92/141, 65.2%) of babies with confirmed neonatal infection had an associated admission to neonatal or (more commonly) paediatric care. Of those admitted to hospital, 6/92 (6.5%) infants were admitted to neonatal or paediatric intensive care, however none of these six had COVID-19 recorded as the main diagnosis underlying their admission. There were no neonatal deaths among babies with confirmed infection. Implications and relevanceConfirmed neonatal SARS-CoV-2 infection is uncommon. Secular trends in the neonatal infection rate broadly follow those seen in the general population, albeit at a lower level. Maternal infection at birth increases the risk of neonatal infection, but most babies with neonatal infection are born to women without confirmed infection. A high proportion of neonates with confirmed infection are admitted to hospital, with resulting implications for the baby, family, and services, although their outcomes are generally good. Key messagesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIThe incidence of SARS-CoV-2 infection in neonates is low, but some studies have suggested that age under 1 month is a risk factor for severe infection requiring admission to intensive care. C_LIO_LIAlmost all the studies of neonatal SARS-CoV-2 have focused on the transmission risk from SARS-CoV-2 positive women to their offspring and data are lacking on the level of neonatal SARS-CoV-2 infection in the whole population. C_LI What this study addsO_LIThis study includes all babies with confirmed SARS-CoV-2 in the neonatal period in Scotland during the first 22 months of the COVID-19 pandemic. C_LIO_LIConfirmed neonatal SARS-CoV-2 infection is uncommon, but a high proportion of neonates with confirmed infection are admitted to hospital. C_LIO_LIConfirmed maternal SARS-CoV-2 infection around the time of birth substantially increases the risk of neonatal infection, although the absolute risk of neonatal infection remains low (<2%) and most babies with neonatal infection are born to women without confirmed infection. C_LIO_LIOutcomes for neonates with confirmed SARS-CoV-2 infection are good; only 6.5% (6/92) of admitted neonates required intensive care, and COVID-19 was not the primary diagnosis recorded for these babies. There were no neonatal deaths among babies with confirmed infection. C_LI