We aim to investigate the differences in physiological characterization between Yo-Yo intermittent recovery test level 1 (Yo-Yo IR1) and level 2 (Yo-Yo IR2) in Japanese college soccer players. Eighty-two Japanese college soccer players (elite, <i>n</i>=40; non-elite, <i>n</i>=42) participated in the study. All subjects took part in three tests Yo-Yo IR1, Yo-Yo IR2, and laboratory treadmill tests. The order of the three tests was randomized across subjects. The Yo-Yo IR1 test was not significantly different between elite (2369.0±319.2 m) and non-elite (2315.2±346.3 m) players. In contrast, the Yo-Yo IR2 test was significantly different between elite (1035.0±147.5 m) and non-elite (919.0±119.3 m) players. Anaerobic threshold (AT) was significantly correlated with both Yo-Yo IR1 and Yo-Yo IR2, although the correlation was stronger for Yo-Yo IR2. Our findings suggest that the Yo-Yo IR2 test will probably be a better tool than Yo-Yo IR1 in measuring endurance capacity in Japanese college soccer players.<br>