The present study was conducted to evaluate the protective effect of seasonal influenza vaccination on the development of influenza-like illness (ILI), as well as to investigate factors related to the development of ILI among patients in a Japanese dialysis facility. One hundred eighty-three hemodialysis (HD) patients were followed up from November 2008 to March 2009. During the follow-up period, 17 patients developed ILI. We compared the characteristics of these 17 patients to patients without ILI. Compared to the non-ILI group (N = 166), the ILI group (N = 17) showed a non-significantly lower rate of influenza vaccination (70.6% vs. 86.7%, P = 0.07), while any other factor did not differ between the two groups. Influenza vaccination tended to reduce the risk of ILI (Odds ratio = 0.37, 95% CI = 0.12 to 1.14, P = 0.07). The findings of the present study suggested that the influenza vaccine was 60% effective to prevent ILI among HD patients, although the effectiveness was not statistically significant.