Alterations in the methylation status of genes may contribute to the progression of Chronic Myeloid Leukemia (CML). In this study, the methylation status in exon2 of SOCS-1 and promoter regions of both SOCS-1 and JUNB were evaluated in CML patients. The methylation status of these genes was analyzed using methylation-specific Polymerase Chain Reaction (MSP) in 30 samples from CML patients, 30 samples from these same patients after hematopoietic stem cell transplantation (HSCT) and 30 samples from healthy controls. The samples of CML patients presented methylation as follows: JUNB gene (3.3%), promoter region of the SOCS-1 gene (6.6%) and exon2 of the SOCS-1 gene (46.6%). The samples of the healthy individuals presented methylation (10%, P = 0.002) only in exon 2 of the SOCS-1 gene. After transplantation, patients presented alterations in the methylation status of the promoter region of the SOCS-1 gene (6.6%), exon2 of SOCS-1 (46.6%) and the promoter region of the JUNB gene (16.6%). Methylation of the promoter regions of the SOCS-1 gene and the JUNB gene is not a frequent event in CML. In contrast, SOCS-1 gene methylation in exon2 is a frequent event, susceptible to alterations in status after HSCT with possible implications for the progression of this disease.