Liver steatosis (also known as fatty liver) is strongly associated with single nucleotide polymorphisms (SNPs) in the patatin-like phospholipase domain containing3 (PNPLA3) gene. The relationship between liver steatosis and PNPLA3 SNP was investigated in the northern part of Okinawa (Yambaru) in light of a report indicating that Okinawa Prefecture has the highest prevalence of liver steatosis in Japan. Abdominal ultrasonography was performed in 178 patients at health check-ups to evaluate liver steatosis based on hepatorenal contrast. The steatosis ratio was higher in males (39.5%) than in females (18.6%; p=0.0020). Among the 178 patients, 74 were selected for PNPLA3 SNP analysis, including 36 with and 38 without liver steatosis, with matching for age and sex between the groups. In the PNPLA3 SNP analysis, the ratios of the TT, GT/TG, and GG alleles were 16.2%, 58.1%, and 25.7%, respectively. Women with liver steatosis had a higher body mass index (p=0.0003) and body fat percentage (p<0.0001) than women without liver steatosis and those with the GG allele had a significantly higher body fat percentage (41.0±6.5%) than those with the TT allele (29.8±7.1%; p=0.0203). Multiple logistic regression revealed a significant relationship between liver steatosis and number of risk alleles G (adjusted odds ratio: 4.549; p=0.0073) as well as body fat percentage (adjusted odds ratio: 1.085; p=0.0329). Furthermore, the higher prevalence of risk alleles (G) in the PNPLA3 gene in Okinawa than in other regions possibly explains the higher prevalence of liver steatosis in Okinawa. Thus, effectively utilizing abdominal ultrasonography in health check-ups, detecting liver steatosis at an early stage, and then providing advice on lifestyle improvements is crucial.