Aim: The aim of this study is to investigate the effect of a 3-day high-carbohydrate diet (≥75% of total calories) on body composition using dual-energy X-ray absorptiometry (DXA). Methods: Twenty non-obese young men (age 22.7 ± 2.6 years, BMI 23.5 ± 2.1 kg/m2) completed the study. Two DXA tests were performed for the measurement of total body weight, body mass index (BMI), body fat percentage as well as total, appendicular and central lean body mass (LBM) before and after a high-carbohydrate diet for 3 days. In addition, the participants completed a food diary during the 3-day high-carbohydrate diet to determine the mean percentage of carbohydrates consumed from total kilocalories. Results: The mean percentage of carbohydrate intake over 3 days was 83.7 ± 8.4%. Our results showed a significant increase in total body weight, BMI as well as total and appendicular LBM after the high-carbohydrate diet (p < 0.01). In addition, we observed a strong tendency for lower body fat percentage values after the intervention (p = 0.05). No significant difference was observed for central LBM. Conclusions: These results indicate that the effect of an acute high carbohydrate diet seems to affect body composition values using DXA, such as total LBM. This study may lead to the need of standardizing a diet prior to using DXA.