Bitterness-sensing protein taste receptor type-2 member 38 (TAS2R38, T2R38) mediates taste perception and various physiological responses, including energy- and adiposity-related mechanisms. This study examined whether the genetic variant rs10246939 C > T in TAS2R38 was associated with food intake and body size as well as obesity risk. Data from the Korean Multi-Rural Communities Cohort study (1338 males and 2229 females) were analyzed to obtain the intake of six food groups, alcohol consumption, smoking status and anthropometric measurements, including height, weight, waist and hip circumference, and body mass index (BMI), according to the rs10246939 genotype. Findings suggested that females with the TT genotype consumed more fruit (adjusted p = 0.025) and had significantly higher body weights (adjusted p = 0.046) and BMIs (adjusted p = 0.003) than individuals with other genotypes. Having the TT genotype also increased the risk of obesity by 1.75-fold (95% confidence interval: 1.31–2.36) in females. The genetic variation had a minimal influence on the males’ dietary intake, but tended to increase the adiposity risk. In conclusion, TAS2R38 rs10246939 variation was associated with Koreans’ dietary intake and increased their risk of obesity. Although more detailed statistical analyses in the larger cohort are required, current study suggested that, as a genetic predictive marker, TAS2R38 bitterness receptor variations may have a large implication in obesity prevention and treatment.