Post-marketing safety surveillance of new vaccines aimed to be administered during pregnancy is crucial to orchestrate efficient adverse events evaluation. This is of special relevance in the current landscape of new vaccines being introduced in the pregnant women population, and particularly due to the recent administration of COVID-19 vaccines in pregnant women. This multi-center prospective cohort study, nested within the WHO-Global Vaccine Safety-MCC study, involved two hospitals in the Valencia region. Hereby, the incidence rates of seven perinatal and neonatal outcomes in the Valencia region are presented. The pooled data analysis of the two Valencian hospitals allowed the estimation of incidence rates in the Valencia Region (per 1000 live births): 86.7 for low birth weight, 78.2 for preterm birth, 58.8 for small for gestational age, 13 for congenital microcephaly, 0.4 for stillbirth, 1.2 for neonatal death and 6.5 for neonatal infection. These figures are in line with what is expected from a high-income country and the previously reported rates for Spain and Europe, except for the significantly increased rate for congenital microcephaly. Regarding the data for maternal immunization, the vaccination status was collected for 94.4% of the screened pregnant women, highlighting the high quality of the Valencian Vaccine Registry. The study also assessed the Valencian hospitals’ capacity for identifying and collecting data on maternal immunization status, as well as the applicability of the GAIA definitions to the identified outcomes.