Background; Congenital malformations like oesophageal atresia (OA) and tracheo-esophageal fistula (TOF), congenital pulmonary airway malformations (CPAMs), congenital diaphragmatic hernia (CDH) and vascular rings (VRs) can influence lung development and respiratory function with significant impact on individuals, families, and health care system. This observational study outlines our multidisciplinary approach and respiratory follow-up for children with these congenital malformations. Methods; We collected clinical data of children followed at the Pediatric Respiratory Unit of Parma University Hospital (Italy) between January 2015 and May 2023. Results; Thirty-five patients have been included. The most common anomalies were AE (n = 12) and CHD (n = 9), followed by CPAMs (n = 9) and VRs (n = 5). In 50% of patients, the diagnosis was made through prenatal ultrasound, particularly in almost all patients with CPAMs (88.8%) and CDH (77.7%), contrary to OE, diagnosed postnatally in the majority of patients (83%). Children underwent their first respiratory visit at an average age of 2.5 years, follow-up was conducted on average every 6 months. More than half of patients (54%) was hospitalized for lower respiratory tract infections, particularly those with OA and those aged <3 years. Eight out of the 16 children capable of performing spirometry showed abnormalities in lung function. Conclusions; Children with congenital malformations are at risk of short and long-term respiratory complications. A personalized follow-up with close collaboration between pediatric pulmonologist, surgeon, neonatologist, physiotherapist is essential to optimize their management and improve their respiratory function.