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Abstract Background Medical students must meet curricular expectations and pass national licensing examinations to become physicians. However, no previous studies explicitly modeled stages of medical students acquiring basic science knowledge. In this study, we employed an innovative statistical model to characterize students’ growth using progress testing results over time and predict licensing examination performance. Methods All students matriculated from 2016 to 2017 in our medical school with USMLE Step 1 test scores were included in this retrospective cohort study (N = 358). Markov chain method was employed to: 1) identify latent states of acquiring scientific knowledge based on progress tests and 2) estimate students’ transition probabilities between states. The primary outcome of this study, United States Medical Licensing Examination (USMLE) Step 1 performance, were predicted based on students’ estimated probabilities in each latent state identified by Markov chain model. Results Four latent states were identified based on students’ progress test results: Novice, Advanced Beginner I, Advanced Beginner II and Competent States. At the end of the first year, students predicted to remain in the Novice state had lower mean Step 1 scores compared to those in the Competent state (209, SD = 14.8 versus 255, SD = 10.8 respectively) and had more first attempt failures (11.5% versus 0%). On regression analysis, it is found that at the end of the first year, if there was 10% higher chance staying in Novice State, Step 1 scores will be predicted 2.0 points lower (95% CI: 0.85–2.81 with P |