Background: In children with primary immunodeficiency (PID), the most common types of infection are respiratory tract infections, among which viral pneumonia representing the majority. Early diagnosis and treatment can prevent or diminish the respiratory complications. Multiplex polymerase chain reaction (Multiplex PCR) can permit amplification of a lot of viruses all together in a single reaction mixture. Objective: Determining different viruses causing pneumonia in children with PID by multiplex PCR. Methodology: A cross-sectional study included 33 nasopharyngeal swabs collected from children suffering from PID with clinical respiratory signs of pneumonia. For each collected sample, nucleic acid extraction and multiplex PCR were done using primers specific for influenza A, influenza B, adenovirus, respiratory syncytial virus (RSV), cytomegalovirus (CMV), parainfluenza virus 1 (PIV1), parainfluenza virus 2 (PIV2), parainfluenza virus 3 (PIV3) and human coronavirus (HCoV-NL63). Results: Viruses were detected in 11 nasopharyngeal samples (11/33, 33.33%). Viral pneumonia was mostly found in children with severe combined immune deficiency (5/11; 45.45%), followed by children with common variable immunodeficiency (3/11; 27.27%) and children with hyper Ig E syndrome, hyper Ig M syndrome and selective Ig A deficiency (1/11; 9.09%) for each. RSV and CMV were the most common detected viruses; each virus was detected in 3 cases. Influenza virus A was detected in 2 cases and adenovirus, PIV1 and PIV3 each was detected in one case. Influenza virus B, PIV2 and HCoV-NL63 were not detected in any sample. No viruses were detected in the nasopharyngeal swabs taken from children with chronic granulomatous disease. No mixed viral infection was detected in any sample. Conclusion: Severe viral pneumonia is frequent in the children with PID. Multiplex PCR has a major benefit, as it allows simultaneous amplification of several viruses in a single reaction mixture with cost-effective diagnosis.