Congenital malformations represent a relevant cause of fetal, neonatal and infant mortality, and morbidity. In consideration of the few resources available, various studies have been conducted to evaluate the different methods of data collection using different information sources. This study aims to improve knowledge on congenital malformations in the Calabria Region in 2017 through the development of a formal procedure to connect and integrate the current SDO and CeDAP flows with the regional register of congenital malformations (RRMC) to enhance different sources information and create a single database. Hospitalization flow of the Calabria Regional Health System have been selected for all those born in the Region in 2017 and their hospitalizations within the first year of life. There were 1,307 cases with at least one ICD-9-CM code in the range 740-759. Cases deemed "minor" were excluded and the "potentially malformed" case search procedures were performed. Following the application of the assessment criteria, 449 cases were considered "validated", 81 cases with malformation in the birth flow and 215 in the Malformation registrer were detected. The various flows contributed to the construction of the integrated regional malformed registe, the integration of the RRMC flow with the hospital discharge cards (SDO) and with the Certificate of Childbirth Assistance (CedAP), has allowed to obtain complete coverage of the birth points of the Calabria Region, for a total of 16,282 births supervised. The birth rate recorded among the supervised births was 4.3 per 1,000. The separate use of information from the registers and from the different health flows, which normally do not communicate with each other, has however shown limits. The records contain detailed descriptions of the malformative condition, but often lack information on surgical interventions or further instrumental clinical investigations. Instead, this information is present in the other streams. On the other hand, the importance of diagnosis and coding of correct malformations, often deficient in SDO and CeDAP, have important implications for research and evaluation purposes.