The body mass index (BMI) is commonly used in the assessment of obesity and overweight; however, its use in the diagnosis of adverse effects of obesity is questioned. This study aims to explore the agreement between the BMI and the calculated body fat percentage (BF%) in detecting obesity-induced ventilatory abnormalities. We carried out a cross-sectional study on a random sample of 150 healthy male students, aged 17 to 25, with a mean age of 20.8 ± 2.6 years. We measured the BMI, BF%, and pulmonary function of each participant. The students were classified into overweight-obese and normal groups based on the BMI and the BF% results. The Chi-square test was performed to analyze differences between the groups. About one-fifth of all participants had a fat mass ≥ 20%, among which 90% fulfilled the BMI definition of overweight and obesity (p < 0.05). The comparison between the two BF% groups showed that 20% of the overweight-obese group had a significant reduction in FEV1 (p= 0.025, Relative Risk= 3.00, 95% Confidence Interval= 1.13-7.99), and 23% of them had a significant reduction in FVC (p= 0.012, Relative Risk= 3.11, 95% Confidence Interval= 1.26-7.68). The changes in FEV1/FVC were statistically insignificant. The effects of the BMI categories on the dynamic lung volumes were statistically insignificant. The direct estimation of BF% is better than the calculation of BMI in the diagnosis of obesity-induced abnormalities in lung function. The use of BMI as an indicator of obesity in population health studies should be avoided.