X-linked agammaglobulinemia (XLA) is an immunodeficiency caused by mutations in the Bruton tyrosine kinase (Btk) gene. In order to identify the mutations in Btk gene in Iranian patients with antibody deficiency, 13 male patients with an XLA phenotype from 11 unrelated families were enrolled as the subjects of investigation for Btk mutation analysis using PCR-SSCP followed by sequencing. Five different mutations were identified in 5 patients from 5 unrelated families. Three mutations had been reported previously including TTTG deletion in intron 15 (4 bps upstream of exon 16 boundary), nonsense point mutation (1896G>A) that resulted in a premature stop codon (W588X) in kinase domain, and nucleotide alteration in invariant splice donor site of exon12 (IVS12+1G>A). While 2 novel missense mutations (2084A>G, 1783T>C) were identified leading to amino acid changes (I651T, Y551H). The results of this study further support the notion that molecular genetic testing represents an important tool for definitive and early diagnosis of XLA and may allow accurate carrier detection and prenatal diagnosis.