The low cost and portability of three-dimensional (3D) infrared body scanners make them an attractive tool for body composition measurement in athletes. The main purpose of this study was to compare total body fat percentage (BF%) and total lean mass (LM in kg), in a cohort of collegiate athletes, using a 3D infrared body scanner versus a dual energy x-ray absorptiometry (DXA) scanner. Phase I was a pre-season cross-sectional analysis of 61 (39 male) athletes while Phase II was a longitudinal subset analysis of 38 (27 male) student-athletes who returned to the laboratory for post-season scans (Post minus pre-season change). Both the 3D and DXA scans were performed within 20-minutes of one another in the same room, wearing the same clothing. Paired t-tests were used to compare the mean values (BF% and LM) between measurement devices with estimated effects size calculated using Cohen's . Data reported as mean±SD. Mean difference (DXA minus 3D) in LM were significantly higher using the 3D scan (5.84 ± 3.55kg; p < 0.001; = 0.90) compared to the DXA scan, while significantly underestimating BF% (-4.57 ± 4.67%; p < 0.001; = 1.6) in Phase I analyses. In Phase II analyses, significant differences in the change (post-season minus pre-season change) values were found between methods for LM (4.45 ± 5.04; < 0.001; = 0.90), while BF% (-0.41 ± 2.06; = 0.223; = 0.2) showed no significant differences. In summary, the 3D and DXA scan values for LM and BF% were not interchangeable in cross-sectional nor longitudinal body composition analyses in collegiate athletes. Close agreement was only observed in longitudinal analyses of BF% and requires further validation with larger cohorts.