Objectives. To examine differences in recidivism rates between different prisons using two designs—between-individual and within-individual—to account for confounding factors. Methods. We examined recidivism rates among 37,891 individuals released from 44 Swedish prisons in three security levels, and who were followed from 2006 to 2013. We used longitudinal data from nationwide registers, including all convictions from district courts. First, we applied a between-individual design (Cox proportional hazards regression), comparing reconviction rates between individuals released from prisons within the same security level, while adjusting for a range of individual-level covariates. Second, we applied a within-individual design (stratified Cox proportional hazards regression), comparing rates of reconviction within the same individuals, i.e., we compared rates after release from one prison to the rates in the same individual after release from another prison, thus adjusting for all time-invariant confounders within each individual (e.g. genetics and early environment). We also adjusted for a range of time-varying individual-level covariates. Results. Results showed differences in the hazard of recidivism between different prisons in between-individual analyses, with hazards ranging from 1.22 (1.05–1.43) to 4.99 (2.44–10.21). Results from within-individual analyses, which further adjusted for all time-invariant confounders, showed minimal differences between prisons, with hazards ranging from 0.95 (0.87–1.05) to 1.05 (0.95–1.16). Only small differences were found when violent and non-violent crimes were analyzed separately. Conclusions. The study highlights the importance of research designs that more fully adjust for individual-level confounding factors to avoid over-interpretation of the variability in comparisons across prisons.