Chronic myeloid leukemia (CML) is characterized by formation of the BCR/ABL fusion gene. The response to therapy may vary because of development of secondary cytogenetic changes or resistance. In addition, suppressor of cytokine signalling (SOCS) proteins is also hypothesized as a cause of resistance and poor prognosis when aberrantly overexpressed. This study aims to determine the incidence and prognostic value of the 9q34 deletion using fluorescence in situ hybridization and SOCS-1 mRNA aberrant expression by PCR in 43 CML patients at different phases of the disease and in 10 normal controls and correlate the data to interferon response. All patients were Philadelphia-positive, deletions of 9q34 were observed in 20.9% of all patients (13.3% chronic phase, 10% accelerated phase and 33.3% in blast crisis). SOCS expressions were positive in 53.4% of all patients (40% chronic phase, 50% AP and 66.67% in blast crisis). Analysing outcome based on 9q34 deletion and SOCS expression status showed a statistically significant difference in overall survival and progression-free survival between those with deletions and those without (P < 0.001) and between those with abnormal SOCS expression and those without (P < 0.001). Deletion of 9q34 and aberrant expression of SOCS-1 are associated with poor prognosis in CML patients with different phases of the disease under interferon therapy.