Lipoblastoma is a rare benign tumor that occurs primarily in infancy and early childhood. We present the rare presentation of a 12 cm sized intramuscular lipoblastoma of the thigh in a 23-year-old patient. On histology, the tumor strongly resembled an atypical lipomatous tumor due to the presence of lipoblasts and atypical stromal nuclei. The very focal lobulation and myxoid change presented the only histological hint towards a lipoblastoma. Cytogenetic and subsequent FISH evaluation of the tumor cells showed a 46,XY, t(8;15) (q12;q25) as chromosomal change with rearrangement of the PLAG1 gene. The present case indicates that lipoblastoma should enter the differential diagnosis of an 'atypical' deep seated fatty tumor in adults. The diagnostic value of cytogenetic/molecular analysis in the differential diagnosis of lipomatous tumors is underscored as well.