With the advancements in neuroimaging techniques, understanding the relationship between brain morphology and behavioral tendencies such as criminal behavior has garnered interest. This research addresses the investigation of disparities in neuroanatomical structures between adolescent offenders and non-offenders and considers the implications of such distinctions regarding offender behavior within adolescent populations. Employing data-driven methodologies, MRI scans of adolescents from Barranquilla, Colombia, were analyzed to explore morphological variations. Utilizing a 1.5 Tesla Siemens resonator (Siemens Healthineers, Erlangen, Germany), T1-weighted MPRAGE anatomical images were acquired and analyzed using a systematic five-step methodology including data acquisition, MRI pre-processing, feature selection, model selection, and model validation and evaluation. Participants, both offenders and non-offenders, were aged 14–18 and selected based on education, criminal history, and physical conditions. The research identified significant disparities in the volumes of 42 brain structures between adolescent offenders (AOs) and non-offenders (NOs), highlighting particular brain regions potentially associated with offending behavior. Additionally, a considerable proportion of AOs emanated from lower socioeconomic backgrounds and showcased marked substance use. The findings suggest that neuroanatomical disparities potentially correlate with criminal behavior among adolescents at a neurobiological level. Noticeable socio-environmental factors, such as lower socioeconomic status and substance abuse, were substantially prevalent among AOs. Particularly, neurobiological deviations in structures like ctx-lh-rostralmiddlefrontal and ctx-lh-caudalanteriorcingulate perhaps represent a link between neurological factors and external stimuli.