Background Primary immunodeficiency diseases (PID) comprise a group of more than 300 diseases that affect development and /or function of the immune system. Objectives The aim of this study was diagnosis of PID among a suspected group of neonates and infants within the first six months of life as well as identifying the warning signs of PID characteristic to this period. Method Fifty neonates presenting with warning signs of PID were enrolled in the study. Results The study revealed that twenty six patients (52%) were diagnosed with Primary Immunodeficiency, T cell/combined immunodeficiency were noted as the most common PID class (88.5%) with fourteen T-B-SCID patients (70%) and six T-B+ SCID patients (30%), phagocytic disorders were estimated to be 7.7% while 3.8% were unclassified immunodeficiency. The mean age of presentation for PID group was 1.42±1.38 months with a diagnostic lag of 3.08±1.78 months. Consanguinity was positive in 76.9% of the PID group. Lower respiratory tract infections, persistent fungal infections and lymphopenia were the most significant warning signs for diagnosing PID with a p value of (0.01). Combined, lower respiratory tract infections, fungal infections and lymphopenia were 12.3 times more likely to be associated with PID. Conclusion Focused screening in high risk neonates proved to be a valuable tool for diagnosis of PID disorders.