Background and aims: We aimed to clarify the relationship between alanine aminotransferase (ALT) level and body composition in Japanese medical health checkups, especially in cases with ALT ≤ 30 IU/L (7569 men and 9497 women). Methods: We categorized our study cohort into four groups: type A (ALT value ≤ 10 IU/L), type B (11 ≤ ALT value ≤ 20 IU/L), type C (21 ≤ ALT value ≤ 30 IU/L) and type D (ALT value > 30 IU/L (ALT over 30)). We retrospectively compared body composition-related parameters (body mass index (BMI), waist circumference (WC), fat (F) index, fatty liver index (FLI), fat-free (FF) index and F-FF ratio) among the four types. Results: Type A/B/C/D in men and women was found in 262/3279/2107/1921 and 1549/5736/1495/717 (p < 0.0001). BMI, WC, F-index, FLI, FF index and F-FF ratio were all significantly stratified among the four types, regardless of whether they were male or female and over or under 50 years old. Conclusions: With a decrease in ALT level in medical health checkups, fat mass decreases, and F-FF ratio decreases, but a decrease in skeletal muscle mass cannot be overlooked.