Mutations that impair early B cell development result in profound antibody deficiency, which is characterized by a paucity of mature B cells and the early onset of recurrent pyogenic infections. Among these inherited early B cell defects, X‐linked agammaglobulinemia (XLA) with mutations in Bruton's tyrosine kinase (BTK) gene is mostly identified. Recent studies have shown that mutations in the gene for μ heavy chain (IGHM) and for other components of the pre‐B cell receptor complex, including λ5/14.1 (IGLL1) or Igα (CD79a), can cause a disorder that is clinically similar to XLA. In a genetic survey of XLA in Turkey, we examined possible mutations in the IGHM, IGLL1, and Igα genes in some male patients with presumed XLA who did not have identifiable BTK mutations. We found an eight‐year‐old boy with a novel homozygous mutation in the Igα gene (IVS2+1G>A) causing B cell defect. This is the second case of agammaglobulinemia due to an Igα (CD79a) deficiency in the world. © 2002 Wiley‐Liss, Inc.