Objectives Rare diseases (RDs) collectively affect approximately 400 million individuals globally, including newborns and children. These conditions often involve genetic, metabolic, or congenital disorders and are challenging to diagnose and manage due to their subtle or non-specific symptoms. Aim is to emphasize the need for specialized, multidisciplinary, and technology-driven approaches to improve outcomes for neonates with RD.Methods A comprehensive review of the infrastructure, diagnostic approaches, and clinical care strategies for RDs in neonates was conducted. The Department of Neonatology and Rare Diseases at the Medical University of Warsaw was analyzed as a model for centralized care, integrating prenatal consultations, advanced diagnostics, and multidisciplinary treatment.Results The department offers specialized care for neonates with RDs, including intensive care, advanced diagnostic tools, and personalized therapies such as pharmacological interventions and surgery. Collaboration with a perinatology center ensures prenatal consultations, delivery planning, and early interventions, while the proximity of operating rooms to neonatal units enhances outcomes. Genetic counseling plays a pivotal role in supporting families and expanding newborn screening programs with emerging osmic technologies which can significantly improve early diagnosis and management.Conclusions Centralized, multidisciplinary care and advancements in diagnostic technologies are essential for improving outcomes for neonates with RD. The integration of clinical care, genetic counseling, and innovative screening programs highlights the importance of specialized centers in addressing the unique challenges of these conditions.