Myeloid sarcoma (MS) is a presentation of acute myeloid leukemia (AML) as a tumor mass outside of the bone marrow. Viable cells from MS are frequently unavailable for cytogenetic studies. We therefore investigated whether chromosomal microarray analysis (CMA) using formalin-fixed paraffin-embedded (FFPE) tissues can detect clinically important genetic abnormalities in MS. CMA successfully identified genomic aberrations in six cases of MS, and in two cases it revealed multiple abnormalities equivalent to a complex karyotype, thus predicting a poor outcome. CMA using FFPE material is therefore a feasible and clinically applicable approach for detection of prognostically significant genomic abnormalities in MS.