Primary immunodeficiency diseases (PID) comprise a heterogeneous group of inherited diseases with a wide spectrum of clinical manifestations and laboratory abnormalities. Definite diagnosis of a PID is performed most reliably by detection of a gene mutation which will allow genetic counseling. In addition, detection and confirmation of PIDs that were not severe enough during childhood to lead to a specific diagnosis would be possible. As a definite diagnosis of PID is of importance for the management of these disorders, we present a review on studies that have investigated mutations among patients with different types of PID in Iran. Although the frequency of a definite molecular diagnosis of PID in Iran is acceptable in a developing country, we believe that providing additional laboratory resources and diagnostic methods, development of specialized centers for PID, in addition to improvement of physicians' awareness, may facilitate clinical and genetic diagnosis of patients with PID in Iran.