Autoimmune neutropenia is a type of immune-mediated neutropenia, caused by antibody-induced neutrophil destruction. Here, we report two cases (a 3-year-old boy and a 9-year-old girl) with suspected autoimmune neutropenia. The presence of neutrophil antibodies in the sera of these two patients was investigated; using standard neutrophil antibody screening tests such as granulocyte immunofluorescence test (GIFT), granulocyte agglutination test (GAT), and lymphocyte immunofluorescence test (LIFT). A positive reactivity with two-panel cells was found in GIFT. No reactivities with panel cells were observed in GAT and LIFT. To the best of our knowledge, this is the first report for detecting the neutrophil reactive antibodies; using genotyped neutrophils in patients with autoimmune neutropenia in Iran. The final diagnosis of our patients was primary autoimmune neutropenia for the boy and autoimmune neutropenia associated with familial Mediterranean fever for the girl.