CD49d is a negative prognosticator in chronic lymphocytic leukemia (CLL), expressed by ~40% of CLL cases, and associated with aggressive and accelerated clinical courses. In the present study, analyzing CD49d expression in a wide CLL cohort (n=1200) belonging to different cytogenetic groups, we report that trisomy 12 CLL almost universally expressed CD49d, and were characterized by the highest CD49d expression levels among all CD49d(+) CLL. Through bisulfite genomic sequencing, we demonstrated that while CD49d(+)/trisomy12 CLL almost completely lacked methylation of the CD49d gene, CD49d(-)/no trisomy12 CLL were overall methylated, the methylation levels being inversely correlated to CD49d expression (p=0.0001). Consistently, CD49d expression was recovered in CD49d(-) hypermethylated CLL cells upon in-vitro treatment with the hypomethylating agent 5-aza-2'-deoxycytidine. These findings may contribute to explain the clinico-biological features of trisomy 12 CLL, including the high rates of cell proliferation and disease progression, lymph node involvement and predisposition to Richter's syndrome transformation.