The most common cause of thrombocytopenia in children is the immune thrombocytopenia, diagnosed in case of typical clinical manifestation and after exclusion of other background. In the case of refractory immune thrombocytopenia, the diagnostic approach should be expanded due to possible other etiology. In the new-born male, thrombocytopenia was discovered immediately after birth. The pregnancy was uncomplicated, and the family did not reveal significant morbidities. During the work-up, the most common causes of thrombocytopenia in neonatal age were excluded, including infectious background, fetal hypoxia, alloimmune thrombocytopenia, and myeloproliferative diseases. The patient was treated according to the recommendations for the management of immune thrombocytopenia, but did not achieve normalization of the platelet number. The genetic testing identified a mutation in the WAS gene (new pathogenic variant NM_000377.2: c.274-1G > A – splice acceptor variant), which allowed to establish the Wiskott-Aldrich syndrome diagnosis. The described case reminds the need for in-depth diagnostics in patients with therapy resistant immune thrombocytopenia.