Purpose: This study was conducted to evaluate the validity of the Gene-Health application in terms of estimating energy and macronutrients. Methods: The subjects were 98 health adults participating in a weight-control intervention study. They recorded their diets in the Gene-Health application, took photographs before and after every meal on the same day, and uploaded them to the Gene-Health application. The amounts of foods and drinks consumed were estimated based on the photographs by trained experts, and the nutrient intakes were calculated using the CAN-Pro 5.0 program, which was named ‘Photo Estimation’. The energy and macronutrients estimated from the Gene-Health application were compared with those from a Photo Estimation. The mean differences in energy and macronutrient intakes between the two methods were compared using paired t-test. Results: The mean energy intakes of Gene-Health and Photo Estimation were 1,937.0 kcal and 1,928.3 kcal, respectively. There were no significant differences in intakes of energy, carbohydrate, fat, and energy from fat (%) between two methods. The protein intake and energy from protein (%) of the Gene-Health were higher than those from the Photo Estimation. The energy from carbohydrate (%) for the Photo Estimation was higher than that of the Gene-Health. The Pearson correlation coefficients, weighted Kappa coefficients, and adjacent agreements for energy and macronutrient intakes between the two methods ranged from 0.382 to 0.607, 0.588 to 0.649, and 79.6% to 86.7%, respectively. Conclusion The Gene-Health application shows acceptable validity as a dietary intake assessment tool for energy and macronutrients. Further studies with female subjects and various age groups will be needed.