A rapidly growing literature has documented the adverse social, economic and, recently, health impacts of experiencing incarceration in the United States. Despite the insights that this work has provided in consistently documenting the deleterious effects of incarceration, little is known about the specific timing of criminal justice contact and early health consequences during the transition from adolescence to adulthood-a critical period in the life course, particularly for the development of poor health. Previous literature on the role of incarceration has also been hampered by the difficulties of parsing out the influence that incarceration exerts on health from the social and economic confounding forces that are linked to both criminal justice contact and health. This paper addresses these two gaps in the literature by examining the association between incarceration and health in the United States during the transition to adulthood, and by using an analytic approach that better isolates the association of incarceration with health from the multitude of confounders which could be alternatively driving this association. In this endeavor, we make use of variable-rich data from The National Longitudinal Study of Adolescent to Adult Health (n = 10,785) and a non-parametric Bayesian machine learning technique- Bayesian Additive Regression Trees. Our results suggest that the experience of incarceration at this stage of the life course increases the probability of depression, adversely affects the perception of general health status, but has no effect on the probability of developing hypertension in early adulthood. These findings signal that incarceration in emerging adulthood is an important stressor that can have immediate implications for mental and general health in early adulthood, and may help to explain long lasting implications incarceration has for health across the life course.