We estimated the excess risk of in-patient hospitalization in a large cohort of persons diagnosed with hepatitis C virus (HCV) infection, controlling for social deprivation. A total of 20 749 individuals diagnosed with HCV in Scotland by 31 December 2006 were linked to the Scottish hospital discharge database, and indirectly standardized hospitalization rates, adjusting for sex, age, year and deprivation were calculated. We observed significant excess morbidity considering episodes for: any diagnosis [standardized morbidity ratio (SMR) 3·4, 95% CI 3·3–3·5]; liver-related diagnoses (SMR 41·3, 95% CI 39·6–43·0); and only non-liver-related diagnoses (SMR 2·14, 95% CI 2·08–2·19). Cox regression analyses of the 2000–2006 data indicated increased relative risks of hospitalization for males [hazard ratio (HR) 1·1, 95% CI 1·0–1·2], older age (per 10 years) (HR 1·55, 95% CI 1·5–1·6), and those testing HIV-positive (HR 1·6, 95% CI 1·3–1·8). This study has revealed substantial excess all-cause and liver-related morbidity in the Scottish HCV-diagnosed population, even after allowing for deprivation.