The components of physical fitness, aerobic capacity and anthropometric characteristics play an important role in maintaining and protecting cardiorespiratory functioning during all stages of life. The purpose of this study was to analyze the relationship between body fat indicators and aerobic capacity of students in a physical education program. A descriptive study (cross-sectional) was carried out with 110 physical education university students (75 males and 35 females). Ages ranged between 17.7 and 26.1 years old. Weight, standing height, sitting height, waist circumference (WC), and seven skinfolds (mm) were evaluated. Body Mass Index (BMI) was calculated. The Navette test (20m back and forth run) was used to assess the students. The correlations between adiposity and aerobic capacity for males varied from r= -0.21 to 0.34 and for females, from r= -0.21 to 0.34. In general, greater body adiposity (BMI, WC, and skinfolds) was a determinant in the males (R2= 14 to 27%). For the females, the Σ 7 skinfolds explained 11% of the adiposity. Males and females classified as having a high level of aerobic capacity showed less fat tissue (Σ 7 skinfolds) than those with moderate and low aerobic capacity (p<0.05). The results from this study indicated that body adiposity expressed as fat tissue limited aerobic capacity in a greater proportion of the males than in the females. The youth classified with high aerobic capacity showed less body fat than their counterparts classified as having moderate and low levels of aerobic capacity.