Purpose Urine is the most common matrix for prisoner drug testing, although oral fluid offers a possible alternative. Identifying new drug intake by a prisoner results in negative sanctions. Detection times in oral fluid after chronic drug intake may be extended. Within the prison admission population are chronic drug users. Our aim was to investigate drugs of abuse detection windows in oral fluid from prisoners. Methods Nineteen frequent drug abusing prisoners provided oral fluid and urine at admission, and each morning for 9 consecutive days. Results The most positive findings were for amphetamine/ methamphetamine, cannabis and benzodiazepines. Maximum detection times in oral fluid were ≥ 9 days for diazepam, methadone and methamphetamine, with corresponding urinary detection times of ≥ 9, 7 and 6 days. Maximum oral fluid detection times were nine days for clonazepam, eight for oxazepam, three for amphetamine and nitrazepam and two for tetrahydrocannabinol, with positive urinary detection times of 8, ≥ 9, 5, 7 and ≥ 9 days, respectively. Cocaine, morphine and 6-acetylmorphine were positive only one day in oral fluid, and one and two days, respectively, in urine, while 6-acetylmorphine was not detected in urine. Conclusion We confirmed oral fluid as a viable matrix for monitoring drugs of abuse in prisoners. Windows of detection for benzodiazepines and amphetamines were up to one week, an important consideration for evaluating oral fluid drug testing results. Some likely new drug exposures were observed based on urine and oral fluid drug results, but there are few data guiding these interpretations.