Vaccination is the best strategy to prevent influenza infection that is a potential cause of morbidity and mortality in immunosuppressed patients. Here, we evaluated the factors that may affect serological response to influenza vaccine in patients who have undergone hematopoetic stem cell transplantation (HSCT). Sixty-one HSCT recipients were included in the study during the 2007-2008 influenza season. Serum samples prior to vaccination and 6-10 weeks after vaccination were collected. Samples were assayed for antibodies to influenza virus A/H1N1, A/H3N2, and B strains by hemagglutination-inhibition assay. The patients were followed in terms of clinical symptoms up to the next influenza season and for adverse effects within a month after vaccination. Overall, pre-vaccine seroprotection rate against all vaccine antigens (A/H1N1, A/H3N2, and B antigens) was 45.1%, post-vaccine seroprotection rate 91% and seroconversion rate was 28.3%. Seroconversion rates were found to be low against B in patients who were vaccinated in the late influenza season (p = 0.018; respectively). Five patients (10.9%) had no immune response against H1N1. Adverse events were reported in 19.6% (n = 9/46) of the patients. In conclusion, the patients should be vaccinated as early as possible in the influenza season, before they are exposed to the virus.