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There is a high prevalence of assault related Traumatic brain injuries (TBI) among incarcerated male adolescents. Untreated TBIs during adolescence can lead to long-term cognitive deficits, criminal justice contact, and correctional placement. These bio-social influences are often overlooked in correctional practices despite evidence that neurological deficits can lead to maladaptive behaviors to adverse environments. This mixed-methods study examines TBI and custodial conduct and custodial discipline among adolescents in the NYC jail system. Quantitative data on 262 inmates was used to identify the prevalence and correlates of TBI. Qualitative data from interviews with 10 inmates was used to understand experiences and perceptions of TBIs, custodial misconduct and custodial discipline. Results identified a 50% prevalence of TBI, mostly from violence, and suggest that neglecting the biological influences of behavior in correctional facilities can misguide effective correctional management. This study presents implications for improved care of inmates affected by a TBI.