ABSTRACT Introduction Academic motivation (AM), motivation in relation to formal studies that as a construct of the self-determination theory (SDT), is frequently assessed by the Academic Motivation Scale (AMS). However, the scoring of AMS in itself is not fully consistent with the SDT theory as only scores of the subscales can be calculated resulting in seven different score means instead of positioning the individual on the self-determination continuum. There have been few attempts at a person-centered approach to AMS scoring, especially among medical students. Our study aimed to find distinct academic motivation profiles and demonstrate their concurrent criterion validity with mental health variables (psychological distress, life satisfaction) among medical students. Methods The AMS-28 college version, the General Health Questionnaire (GHQ-12), and the Single-Item Measure of Life Satisfaction were administered among medical freshmen. Academic motivation profiles were generated by two methods: 1) two-step cluster analysis, and 2) quantile analysis. Results The sample consisted of 189 participants (mean age = 19.38 ± 2.03 years, 72% females). The cluster analyses revealed three fairly distinct profiles of self-determination: ‘High’ (n = 59; mean im = 5.48 ± 0.60; mean em = 6.07 ± 0.41; mean am = 1.57 ± 0.95), ‘Moderate’ (n = 111; mean im = 4.5 ± 1.06; mean em = 4.41 ± 0.87; mean am = 1.25 ± 0.36), and ‘Low’ (n = 19; mean im = 4.22 ± 1.02; mean em = 4.03 ± 1.16; mean am = 3.07 ± 1.30). The creation of deciles allowed the identification of those who were most intrinsically (n = 14, 7.4%), extrinsically (n = 10, 5.3%), and least motivated (amotivated) (n = 18, 9.5%). ‘Low’ self-determination/amotivation was associated with increased psychological distress and decreased life satisfaction. Conclusion Our results provide means to position medical students on the SDT continuum based on ‘Low’, ‘Moderate’, or ‘High’ levels of self-determination toward their studies. These AM profiles predict the mental health of medical freshmen, which supports the validity of the outcomes and highlight the risks of amotivation for psychological morbidity. The limitations and implications are discussed.