This study examines potential differences in the mental health, pro-inflammatory cytokines and brain-derived neurotrophic factor (BDNF) of patients with hepatitis C virus (HCV) infection who underwent antiviral treatment with peginterferon-alpha-2a (PegIFN-α-2a) and peginterferon-alpha-2b (PegIFN-α-2b). Methods: In a 24 week non-randomized longitudinal study, 22 patients with HCV were treated with PegIFN-α-2a plus ribavirin (Group A), and 12 patients were treated with PegIFN-α-2b plus ribavirin (Group B). All patients were assessed on the Hospital Anxiety and Depression Scale (HADS), the Short-form Health-related Quality of Life (SF-36) questionnaire, and their serum levels of interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-α), interleukin-1-beta (IL-1β) and BDNF were compared at baseline and weeks 4, 12 and 24. Results: During the 24-week antiviral treatment, Group A and Group B exhibited similar rates of sustained virological response, increased depression levels, decreased scores of physical component summary (PCS) of the SF-36 and reduced serum BDNF levels. However, increased serum levels of IL-6, TNF-α, and IL-1β were observed only in Group A at the 24 th week. During the treatment period, the depression scores and PCS scores of the SF-36 were positively correlated with IL-6, TNF-α and IL-1β levels, and negatively correlated with BDNF levels. Anxiety scores of the HADS were positively correlated with TNF-α and IL-1β levels. Conclusion: This investigation provides insight into the differential effects of various peginterferon-alpha During antiviral treatment, IFN-α activates proinflammatory cytokines and contributes to the development of depressive symptoms [31]. A clinical study found that serum levels of BDNF declined in HCV patients who were undergoing 24 weeks of IFN-α treatment. Accompanying increased levels of pro-inflammatory cytokines were correlated with the development of depressive symptoms [32]. Some investigations have also suggested that IFN-induced depression is accompanied by immune activation and the