Because we observed a reduced humoral immune response to the COVID-19 vaccine and subsequently discovered a lower susceptibility to COVID-19 in individuals carrying the ALDH2 rs671 variant, we hypothesized that rs671 is beneficial for cellular immunity against COVID-19. Using the IFN-γ enzyme-linked immunospot (ELISPOT) assay, we evaluated cellular immunity before and after COVID-19 vaccination in two subcohorts of a previously reported cohort. Subcohort 1 (26 participants) had six repeated observations at baseline and after one to three doses, whereas subcohort 2 (19 participants) had two observations, before and after the third dose. ELISPOT counts at six months after the second dose increased from baseline in carriers of the rs671 variant, but not in non-carriers. A positive effect of rs671 on ELISPOT counts was estimated using a mixed model, including the random effect of subcohort, repeated measures, and fixed effects of vaccine type, age, sex, height, lifestyle, steroid use, and allergic disease. There was no association between ELISPOT counts and specific IgG levels, suggesting a limitation in estimating protective potential by humoral response. There is lower humoral and higher cellular immunity against SARS-CoV-2 in rs671 variant carriers compared to non-carriers, providing a potential basis for optimizing preventive measures and drug discovery.