Background The objective of the study was to estimate the rate of borderline personality disorder (BPD) in male and female offenders newly committed to the Iowa Department of Corrections. We also compared clinical and demographic characteristics of offenders with and without BPD. Methods A random sample of 220 offenders entering Iowa's prison system were evaluated by using a version of the Mini International Neuropsychiatric Interview, the BPD module of the Structured Interview for DSM-IV Personality Disorders, the Medical Outcome Survey Short Form-36 Health Survey, and the Level of Service Inventory-Revised. Results Borderline personality disorder was present in 65 (29.5%) subjects, although 93.2% had at least one Diagnostic and Statistical Manual of Mental Disorders-IV BPD trait. The percentage of women meeting criteria for BPD was more than twice that for men. Subjects with BPD were more likely than those without to be married, employed, and to have a high suicide risk score. Offenders with BPD were more likely than others to report prior mental health treatment, and to have reported high levels of interference from their mental disorder. Offenders with BPD had worse quality of life than offenders without BPD as assessed with the Medical Outcome Survey Short Form 36 Health Survey, and higher rates of mood, anxiety, psychotic, and eating disorders; antisocial personality disorder; and attention deficit hyperactivity disorder. Borderline personality disorder was also associated with higher Level of Service Inventory-Revised total scores, which indicates their having a greater risk for recidivism than nonborderline offenders. These relationships were observed after adjusting for sex, age, race/ethnicity, and presence of antisocial personality disorder. Conclusion Borderline personality disorder is relatively common among both male and female offenders in prison, and is associated with substantial psychologic stress and impaired quality of life. Early recognition and treatment of BPD in prisons may be warranted.