Myxoid liposarcoma is the second most common liposarcoma. Although myxoid liposarcoma is relatively chemosensitive and thus a good candidate for chemotherapy, cases with relapsed or metastatic disease still have poor outcome. Here, we performed a gene microarray analysis to compare the gene expression profiles in six clinical myxoid liposarcoma samples and three normal adipose tissue samples, and to identify molecular biomarkers that would be useful as diagnostic markers or treatment targets in myxoid liposarcoma. This showed that the cancer‐testis antigen PRAME was up‐regulated in myxoid liposarcoma. We then performed immunohistochemical, western blotting and real‐time polymerase chain reaction analyses to quantify the expression of PRAME and another cancer‐testis antigen, NY‐ESO‐1, in clinical samples of myxoid liposarcoma (n = 93), dedifferentiated (n = 46), well‐differentiated (n = 32) and pleomorphic liposarcomas (n = 14). Immunohistochemically, positivity for PRAME and NY‐ESO‐1 was observed in 84/93 (90%) and 83/93 (89%) of the myxoid liposarcomas, and in 20/46 (43%) and 3/46 (7%) of the dedifferentiated, 3/32 (9%) and 1/32 (3%) of the well‐differentiated and 7/14 (50%) and 3/21 (21%) of the pleomorphic liposarcomas, respectively. High immunohistochemical expression of PRAME and/or NY‐ESO‐1 was significantly correlated with tumour diameter, the existence of tumour necrosis, a round‐cell component of >5%, higher histological grade and advanced clinical stage. High PRAME and NY‐ESO‐1 expression correlated significantly with poor prognosis in a univariate analysis. The myxoid liposarcomas showed significantly higher protein and mRNA expression levels of PRAME and NY‐ESO‐1 (CTAG1B) than the other liposarcomas. In conclusion, PRAME and NY‐ESO‐1 (CTAG1B) were expressed in the vast majority of myxoid liposarcomas, and their high‐level expression correlated with tumour grade and poor prognosis. Our results support the potential use of PRAME and NY‐ESO‐1 as ancillary parameters for differential diagnosis and as prognostic biomarkers, and indicate that the development of immunotherapy against these cancer‐testis antigens in myxoid liposarcoma would be warranted.