Survival rates of patients with visceral congenital malformations have increased considerably. However, long-term morbidity in these patients is high. In the last decades, these circumstances have led to a shift in goals of caretakers and researchers with a new focus on patients’ perspectives and long-term morbidity. Health-related quality of life (HrQoL) is the most commonly used patient-reported outcome measure to assess the impact of chronic symptoms on patients’ everyday lives. Most pediatric surgical conditions can cause a significantly decreased HrQoL in affected patients compared to the healthy population. In order to guarantee life-long care and to minimize the impact on HrQoL a regular interdisciplinary follow-up is obligatory. The period of transition from child-centered to adult-oriented medicine represents a critical phase in the long-term care of these complex patients. This scoping review aims to summarize relevant pediatric surgical conditions focusing on long-term-morbidity and HrQoL assessment in order to demonstrate the necessity for a well-structured and standardized transition for pediatric surgical patients.