To examine whether the level of complexity of the services structure and sociodemographic and clinical characteristics of patients in hemodialysis are associated with the prevalence of poor health self-assessment. In this cross-sectional study, we evaluated 1,621 patients with chronic terminal kidney disease on hemodialysis accompanied in 81 dialysis services in the Brazilian Unified Health System in 2007. Sampling was performed by conglomerate in two stages and a structured questionnaire was applied to participants. Multilevel multiple logistic regression was used for data analysis. The prevalence of poor health self-assessment was of 54.5%, and in multivariable analysis it was associated with the following variables: increasing age (OR = 1.02; 95%CI 1.01–1.02), separated or divorced marital status (OR = 0.62; 95%CI 0.34–0.88), having 12 years or more of study (OR = 0.51; 95%CI 0.37–0.71), spending more than 60 minutes in commuting between home and the dialysis service (OR = 1.80; 95%CI 1.29–2.51), having three or more self-referred diseases (OR = 2.20; 95%CI 1.33–3.62), and reporting some (OR = 2.17; 95%CI 1.66–2.84) or a lot of (OR = 2.74; 95%CI 2.04–3.68) trouble falling asleep. Individuals in treatment in dialysis services with the highest level of complexity in the structure presented less chance of performing a self-assessment of their health as bad (OR = 0.59; 95%CI 0.42–0.84). We showed poor health self-assessment is associated with age, years of formal education, marital status, home commuting time to the dialysis service, number of self-referred diseases, report of trouble sleeping, and also with the level of complexity of the structure of health services. Acknowledging these factors can contribute to the development of strategies to improve the health of patients in hemodialysis in the Brazilian Unified Health System.