This review focused on genetic polymorphisms that may be associated with susceptibility to functional dyspepsia (FD), based primarily on studies conducted in Japanese populations. G-proteins β3 (GNβ3) polymorphisms have been most frequently reported to be associated with FD. The higher frequency of s/l and l/l SCL6A4 genotypes in women patients with epigastric pain syndrome and the l/l genotype in postprandial distress syndrome patients was reported. The primiR325 s5981521 T homozygotes leading to reduced post-transcriptional regulation of SCL6A4 are possibly associated with FD. TRPV1G315C, SCN10A 2884G, 3275C, and 3218CC are also possible candidate single-nucleotide polymorphisms (SNPs). Genetic polymorphisms associated with FD vary in frequency among different ethnicities and countries, and no consensus has been reached regarding the association between these polymorphisms and the disease. In addition, the associations between GHRL and COX-1 SNPs and subtypes of FD were reported. However, genetic polymorphisms associated with FD vary in frequency among different ethnicities and countries, and no consensus has been reached regarding the association. Recent genome-wide association studies (GWAS) have reported genetic correlations and overlaps between gastrointestinal and psychiatric disorders, highlighting the role of the brain–gut axis. Further GWAS may lead to applications in personalized medicine.