Background The prevalence of cigarette smoking among incarcerated adult men and women is three-four times higher than in the general population, ranging from 70-80%. However, little is known about factors associated with smoking among incarcerated adolescents, especially upon their re-entry into communities after release from jail. The current study explores factors associated with smoking among adolescent males prior to incarceration and one year after their release from jail. Methods We conducted a secondary data analysis of the Returning Educated African-American and Latino Men to Enriched Neighborhoods (REAL MEN) study, which was designed to reduce HIV risk, substance use, and recidivism among 16–18 year old males leaving jail. We examined differences between smokers and non-smokers at the time of their incarceration (N = 552) and one year after their release from jail (N = 397) using t-tests and chi-square tests. Using logistic and linear regression we examined factors associated with current smoking status, frequency of smoking, and quantity of cigarettes smoked per day both prior to the young men’s incarceration and one year after their release from jail. Results Prior to incarceration, 62% of the young men reported smoking, and one-year after jail release, 69% reported smoking. Prior to incarceration, foster care history, not living with parents, not attending school, drug sales, number of sex partners, gang involvement, current drug charges, and number of prior arrests were positively associated with smoking indicators prior to incarceration. Having violent charges was inversely associated with smoking indicators prior to incarceration. One-year after release from jail, foster care history and number of prior arrests before the index incarceration were associated with smoking indicators. Conclusions Several problem behaviors may be associated with adolescent males’ smoking behaviors prior to incarceration. However, the young men’s histories of difficult life circumstances and engagement in illegal activity may have long-term consequences on smoking for these young men during their transition between jail and community. Findings suggest a need for comprehensive risk reduction interventions in settings in which disadvantaged young men are institutionalized, starting in childhood.