Objectives: We aimed to determine the frequency of SARS-CoV-2 positivity in newborns born to mothers with peripartum SARS-CoV-2 infection in a German cohort, to identify potential risk factors associated with neonatal SARS-CoV-2 infection, and to present short-term outcomes of newborns with vertical transmission of SARS-CoV-2. Methods: Data on women with SARS-CoV-2 infection occurring anytime during their pregnancy was gathered prospectively within the CRONOS registry. From April 2020 to February 2023 a total of 8,540 women had been registered. The timing and the probability of mother-to-child transmission in neonates born to women with perinatal SARS-CoV-2 infection were classified using the WHO classification system. The severity of maternal infection, maternal vaccination status, type of dominant virus, and perinatal outcome parameters were analyzed as potential risk factors for neonatal SARS-CoV-2 infection. Results: 6.3 % resp. 42.9 % of tested newborns and stillbirths were SARS-CoV-2 positive. 2.1 % of newborns with confirmed and possible SARS-CoV-2 infection were identified. Severe maternal COVID-19 (odds ratio 4.4, 95 % confidence interval 1.8-11.1) and maternal infection with the Delta virus (OR 3.2, 1.4-7.7) were associated with neonatal SARS-CoV-2 infection. Newborns with a confirmed or possible infection were significantly more often admitted to the NICU (65.2 % neonatal infection vs. 27.5 % non, p<0.001). Conclusions: The rate of neonatal SARS-CoV-2 positivity was higher in our cohort than previously reported, neonatal SARS-CoV-2 infections were rare. Our data emphasizes con-firmative testing should be performed in newborns of SARS-CoV-2 infected mothers to identify neonatal SARS-CoV-2 infection as an underlying pathology leading to NICU admission.