Congenital anomalies (CAs) are an important cause of infant mortality and efficient surveillance is necessary for their prevention. Therefore, the objective of this study is to establish baselines of prevalence at birth of priority CAs for surveillance in the state of Santa Catarina, using data from the Live Birth Information System considering the period 2011-2019 (baseline) and 2020 (pandemic year). The analyses were carried out based on the mother's residence health macroregion. The CAs were selected following the ICD-10 coding for chapter XVII. Birth prevalence was calculated per 10,000 live births and the confidence interval was established at 95%. 2011-2019 recorded 88.8/10,000 births with CAs (total). For 2011-2019, limb defects (without polydactyly) were the most prevalent (14.1/10,000), followed by congenital heart defects (8.9), oral clefts (8.2), polydactyly (7.9), Down syndrome (5.6), hypospadias (5.4), neural tube defects (4.7), gastroschisis (3.3), undefined sex (1.2), microcephaly (0.8) and omphalocele (0.3). There were no significant differences in temporal and spatial distribution. However, unusual fluctuations were observed in 2020, which may reflect the pandemic in CAs notifications. In the base period, Santa Catarina recorded CAs below the expected level of being identified at birth. With this, we conclude that the training and awareness of teams are essential for the surveillance of CAs in Santa Catarina.