BACKGROUND: Congenital anomalies are among the common health problems faced by children in low- and middle-income countries, contributing substantially to infant mortality rates. Due to limited access to newborn screening programmes in most of the resource-limited settings, many congenital anomalies go undiagnosed and untreated, leading to adverse outcomes. This study aimed to develop and validate a newborn screening tool for congenital anomalies for use in resource-limited settings. METHODS: A Delphi approach was used to assemble a group of experts and develop the screening tool. Tool validation was done by applying it to a reasonable number of neonates who were delivered and/or admitted to the neonatal intensive care unit of St. Paul's Hospital Millennium Medical College. Data were collected using Kobo Collect and then exported to Microsoft Excel and SPSS V.26 for analysis. Frequencies, percentages, mean and SD were used to describe categorical results. The sensitivity and specificity of the screening tool were calculated to assess its validity. RESULTS: A total of 1160 neonates were screened for congenital anomalies, of which 673 (58%) were male. The mean age of the newborns was 26.9±33 hours. Term newborns accounted for 898 (77.4%) of the study population. The prevalence of congenital anomalies in our series was 5.7%, with the most involved body systems being the central nervous system (33.7%), genitourinary (18.5%), gastrointestinal (11%) and musculoskeletal (11%). More than one anomaly was diagnosed in 11 (13.6%) neonates. The sensitivity and specificity of this tool were 86.4% and 97.8%, respectively. Furthermore, the positive and negative predictive values of the screening tool were 70.4% and 99.2%, respectively. CONCLUSION: Congenital anomalies are not rare findings in our hospital. The neonatal screening tool, which was developed through this study, has commendable validity results in addition to being low-cost and easily implementable.