People who inject drugs (PWID) are disproportionately represented among individuals who experience imprisonment and often have more complex physical and mental health needs than people in prison without injecting histories. The trajectories of PWID after prison release are poorly understood, hampering the development of effective strategies to address their distinct health needs. The Prison and Transition Health (PATH) Cohort Study is characterising the post-release trajectories of incarcerated male PWID in Victoria, Australia. We outline study methodology and baseline characteristics of participants prior to their release. Four hundred participants were recruited from three prisons and completed researcher-administered baseline interviews covering socio-demographics, social supports, physical health, mental health, alcohol and other drug use, and pre-release and transitional service utilisation. The median age among participants was 36 years (IQR 30–42), and they reported a median of five (IQR 3–9) previous adult incarcerations. Almost half (49%) were reliant on government payments prior to incarceration. One quarter (25%) of participants reported removal from their parents’ care as children and 64% reported being a parent or primary caregiver to children. Most participants (81%) reported a previous mental health diagnosis and 44% reported three or more diagnoses. The most common drugs injected prior to incarceration were crystal methamphetamine (80%) and heroin (62%), and most (85%) reported being under the influence of drugs at the time of committing offences for which they were currently incarcerated. Injecting drug use during their current sentence was reported by 40% of participants, and 48% reported engaging with some form of drug treatment during their current sentence. Study participants are characterised by significant mental health and substance use morbidities, social disadvantage and criminogenic histories that present challenges for the provision of post-release support services. Data from the PATH Cohort Study will help inform strategies to improve the health and social outcomes of this population.