Muscle mass is an important factor influencing the activity of daily living in older adults. We aimed to investigate whether alpha-actinin-3 (ACTN3) gene R577X polymorphism affects muscle mass in older Japanese women. A total of 109 women (mean+/-SD, 64.1+/-6.0 years) were genotyped for the R/X variant of ACTN3. Mid-thigh muscle cross-sectional area (CSA) was assessed using MRI and compared using analysis of covariance models adjusted for body weight. In addition, physical activity and protein intake were measured as the living environmental factors affecting muscle mass. The ACTN3 R577X genotype distributions of the subjects were 19, 63 and 27 for the RR, RX, and XX genotypes, respectively. No differences in physical activity and protein intake were observed among the genotypes. The XX genotype showed lower thigh muscle CSA compared with RR&RX genotype (mean+/-SEM; XX: 69.1+/-1.8 cm(2), RR&RX: 73.6+/-1.1 cm(2); p<0.05). The results of the present study suggest that ACTN3 R577X polymorphism influences muscle mass in older Japanese women.