Cell death–inducing DNA fragmentation factor α–like effector A (CIDEA) regulates energy expenditure in the adipose tissue and is implicated in the development of obesity. A single nucleotide polymorphism in the CIDEA gene that causes an amino acid substitution of valine 115 to c(V115F) has recently been shown to be associated with obesity in the Swedish population. Here, we determined the effects of this polymorphism on phenotypes of metabolic syndrome within the Japanese population. Two hundred seventy unrelated Japanese male workers (mean age, 44.5 years) were analyzed in a cross-sectional study. The clinical features regarding metabolic syndrome, as well as CIDEA V115F polymorphism, were determined for each individual. The V115F polymorphism associated with waist circumference and fasting plasma glucose. These parameters were at higher levels in the VF + FF group than in the VV group (P < .05). The VF + FF group compared with the VV group had a higher prevalence for abdominal obesity (odds ratio [OR] = 1.89; 95% confidence interval [CI], 1.03-3.44), high fasting plasma glucose (OR = 2.81; 95% CI, 1.03-7.67), and metabolic syndrome (OR = 3.15; 95% CI, 1.05-9.48). These results suggest that the F allele of the CIDEA gene may serve as a risk factor for phenotypes related to metabolic syndrome in Japanese men.