The Polycomb group (PcG) of genes is important for differentiation and cell‐cycle regulation and is aberrantly expressed in several cancers. To analyse the role of deregulated PcG genes in acute myeloid leukaemia (AML), we determined by RQ‐PCR the expression of the PcG genes BMI‐1, MEL18, SCML2, YY1 and EZH2, and the downstream PcG targets HOXA4, HOXA9 and MEIS1 in diagnostic bone marrow samples from 126 AML patients. There was a general overexpression of the genes in AML patients compared to 20 healthy donors, except of HOXA4 and MEL18, which both displayed a wide range of expression levels within the AML subgroups. Among the AML patients with normal karyotype, a low HOXA4 level was associated with a shorter overall survival (P = 0.005). In addition, expression levels of MEL18 and EZH2 were significantly (P < 0.025) higher in patients with complex karyotype and lower in CBF‐mutated patients. The t(8;21) vs. inv(16) positive patients showed significantly different expression of SCML2, BMI‐1, YY1, HOXA9 and MEIS1 (P ≤ 0.01). Comparisons between the PcG and PcG‐regulated genes and a number of clinical and molecular data revealed correlations to genes involved in DNA methylation (DNMT1, DNMT3B), apoptosis (BAX, CASPASE 3) and multidrug‐resistance (MDR1, MRP ) (P < 0.01). In conclusion, our data suggest that the role of PcG and PcG‐regulated genes in leukaemogenesis varies between, as well as within karyotypic subgroups.