Abstract: Congenital hypothyroidism (CH) represents a significant public health concern due to its potential to cause preventable mental retardation. Early detection through screening programs is crucial, as it allows prompt initiation of treatment before irreversible damage occurs. In Sri Lanka, the Ministry of Health has implemented a nationwide screening program using TSH assay methods (Radioimmunoassay – RIA or Enzyme-Linked Immunosorbent Assay – ELISA) to identify infants at risk. This study focuses on evaluating the challenges encountered in the CH screening program at Teaching Hospital Mahamodara (THM) and District General Hospital – Matara, with the objective of improving service delivery.