The purpose of this study was to examine the effects of pre-university adiposity and physical fitness on changes of body weight and adiposity during the freshmen year. Twenty-nine freshmen (sixteen females and thirteen males) completed the study. Body weight and composition (dual-energy X-ray absorptiometry), waist circumference (WC), energy intake (7 d food diary) and activity-related energy expenditure (accelerometry) were measured in September, December and at the end of March. Peak oxygen uptake (VO2peak) was assessed at baseline only. Significant increases in body weight (1·9 (sd 2·0) kg, P < 0·05), BMI (0·6 (sd 0·7) kg/m2, P < 0·05), WC (2·7 (sd 3·0) cm, P < 0·05) and % body fat (BF) (3·1 (sd 2·3) %, P < 0·01) were noted in males, especially over the course of the first semester. No significant changes were observed in females. Results from correlation analyses showed that, baseline %BF was negatively associated with changes in body weight (r − 0·53, P < 0·01) and %BF (r − 0·41, P < 0·05) over the academic year. Baseline %BF predicted 27 % (P < 0·05) of the change in weight. Alcohol intake explained 34 % (P < 0·01) and 17 % (P < 0·05) of the changes in WC and %BF, respectively. The change in body weight and %BF were also positively associated with baseline VO2peak (r 0·51, P < 0·01; r 0·48, P < 0·01, respectively) while dietary restraint was negatively related to the changes in %BF (r − 0·43, P < 0·05). In summary, lower pre-university adiposity, higher VO2peak and higher alcohol intake are associated with greater changes in adiposity and body weight during the freshmen year.