Background: Mental illness is common among prisoners, but little evidence exists regarding changes in symptoms in custody over time. Aims: To investigate the prevalence and predictors of psychiatric symptoms among prisoners during early custody. Method: In a prospective cohort study, 3079 prisoners were screened for mental illness within 3 days of reception. To establish baseline diagnoses and symptoms, 980 prisoners were interviewed; all remaining in custody were followed up 1 month and 2 months later. Results: Symptom prevalence was highest during the first week of custody. Prevalence showed a linear decline among men and convicted prisoners, but not women or remand prisoners. It decreased among prisoners with depression, but not among prisoners with other mental illnesses. Conclusions: Overall, imprisonment did not exacerbate psychiatric symptoms, although differences in group responses were observed. Continued discussion regarding non-custodial alternatives for vulnerable groups and increased support for all during early custody are recommended.