X-Linked thrombocytopenia (XLT) is characterized by congenital thrombocytopenia with small platelets and absence of immunodeficiency; XLT is an allelic variant of Wiskott-Aldrich syndrome (WAS). Both entities are caused by mutations in the same gene. This study presents the case of an 8-year-old boy with XLT. He developed immunoglobulin A (IgA) nephropathy at the age of 4 years. Genetic analysis confirmed the XLT diagnosis. His maternal uncle also had thrombocytopenia from early infancy and developed end-stage renal failure as a result of IgA nephropathy. The maternal uncle was inferred to be affected with XLT because of the carrier status of the patient's mother. Abnormal glycosylation has a role in pathogenesis in IgA nephropathy; moreover, sialophorin glycosylation is defective in WAS. Altered glycosylation may contribute to renal involvement in patients with WAS/XLT despite different defective glycosylation patterns in IgA nephropathy and WAS/XLT.