AimsWe estimated the prevalence of substance use disorders (SUDs) in the Norwegian, Danish and Swedish prison populations and compared the prevalence of SUDs in the national prison populations with country‐specific general population prevalence rates.DesignA multi‐national cohort study using data from the National Prison Registries linked to the National Patient Registries in Norway, Denmark and Sweden.Setting and participantsWe used data from the PriSUD‐Nordic study, including national prison populations aged 19 years and older in Norway (2010–19), Denmark (2010–18) and Sweden (2010–13). A total of 119 507 Individuals (108 971 men and 10 536 women) contributing to 191 507 incarcerations were included in the study (Norway: 45432 men; 5429 women, Denmark: 42 162 men; 3370 women, Sweden: 21 377 men; 1737 women).MeasurementWe calculated a study prevalence and prevalence at entry to prison for all types of SUDs before imprisonment each consecutive year of observation in each prison population. We also extracted country‐specific 1‐year prevalence rates from the Global Burden of Diseases database to calculate comparative national prevalence ratios.FindingsThe study prevalence of any SUD was approximately 40% [Norway: 44.0%, 95% confidence interval (CI) = 43.6–44.5%; Denmark: 39.9%, CI = 39.5–40.4%; Sweden: 39.1%, CI = 38.4–39.7%] in all three countries. Women had a significantly higher study prevalence of any SUD compared with men (Norway: 55.8 versus 42.6%, P < 0.001; Denmark 43.1 versus 39.7%, P = 0.004; Sweden: 51.7 versus 38.0%, P < 0.001). Prevalence estimates were higher for SUDs among people in prison than in the general population. We observed an increasing proportion of people with SUDs entering prison in Norway (P = 0.003), while the proportion was more stable in Denmark and Sweden.ConclusionsSubstance use disorders (SUDs) appear to be highly prevalent among the Scandinavian prison populations compared with the general population, especially among women. In Norway, there was a relative increase in SUDs from 2010 to 2019.