Chondromyxoid fibroma is a rare benign tumor accounting for 1-2% of primary bone tumors. Most of the patients are young males in the 2nd and 3rd decades of life. Metaphyses of long bones are predominantly affected. The histology of this tumor is well established, but its genetic mechanism remains poorly characterized. To our knowledge, only 22 abnormal cytogenetic analyses have been reported, and all contained diploidy or near-diploidy karyograms as their primary event, and inv(6)(p25)(q13) and rearrangements involving regions 6p23-25, 6q12-15, and 6q23-27 constituted a recurrent observation. In this report, a pseudotetraploidy tumor clone with multiple numerical and structural aberrations involving 6p23 as well as other chromosomal loci was identified in a chondromyxoid fibroma from the metaphysis of the left fibula of an 18-year-old male, which has not been reported. The finding may relate to the atypical-looking large cells often seen in this benign tumor.