The epidemiology of hepatitis B virus (HBV) and hepatitis C virus (HCV) is important for health planners and service providers. A cross-sectional study was conducted to investigate the seroprevalence and associated risk factors for markers of HBV (HBsAg) and anti-HCV among hemodialysis patients at the Ahmed Gasim hemodialysis unit, Sudan. Structured questionnaires were used to obtain socio-demographic data and sera were tested for hepatitis B surface antigen (HBsAg) and antibody to HCV (anti-HCV). Of the 353 patients enrolled in the study, HBsAg and anti-HCV were detected in 16 (4.5%) and 30 (8.5%) patients, respectively. None of the patients were co-infected with HBV and HCV. Multivariate analysis showed that duration of dialysis was significantly associated with anti-HCV seropositivity [OR = 1.1, 95% CI = 1.2-1.3; P = 0.024]. No other socio-demographic or clinical characteristics (age, sex, level of education, history of surgery, and number of units of blood transfused) were significantly associated with HBsAg or anti-HCV seropositivity. The results of this study suggest that HBsAg and anti-HCV have low prevalence among hemodialysis patients in Khartoum. Longer duration of dialysis was a risk factor for anti-HCV.