Background Genetic polymorphisms may be associated with infections, and some genes are known to be associated with pneumonia. Aspiration pneumonia is one of the major complications after stroke, and this study aimed to evaluate genetic effects on post-stroke aspiration pneumonia. Methods Blood samples were obtained from a total of 206 post-stroke participants (males, n = 136; mean age, 63.8 years). Genotyping was done for catechol-O-methyltransferase (rs4680 and rs165599), dopamine receptors (DRD1; rs4532, DRD2; rs1800497, DRD3, rs6280), brain-derived neurotrophic factor (rs6265), apolipoprotein E (rs429358, rs7412), and the interleukin-1 receptor antagonist gene (rs4251961). The subjects were stratified into two groups, aged < 65 (young) and ≥ 65 (elderly) years. Functional parameters and swallowing outcomes were measured at enrollment and 3-months post-onset. The primary outcome was the incidence of aspiration pneumonia. Results Analysis of the association between genetic polymorphisms and aspiration pneumonia history showed that a minor C rs429358 allele was associated with the occurrence of aspiration pneumonia in the young group, both in the additive and dominant models (odds ratio [OR], 4.53; 95% Confidence Interval [CI]: 1.60 – 12.84, P = 0.004). In the multivariable logistic analysis, a minor C rs429358 allele increased the risk of post-stroke aspiration pneumonia by 5.35 (95% CI: 1.64 – 20.88). In contrast, no genetic effects were seen in the elderly group. Conclusions A minor C rs429358 allele in young age stroke patients may increase the incidence of post-stroke aspiration pneumonia. Genetic polymorphism may provide useful information on how certain individuals are at increased risk of post-stroke aspiration pneumonia. Clinical Trial Registration-URL: https://www.clinicaltrials.gov. Unique identifier: NCT0357744