This data covers all relevent clinical data of the study "Humoral immune response to tick-borne encephalitis vaccination in allogeneic blood and marrow graft recipients". The full study protocol of this study is published at clinicaltrials.gov ((https://clinicaltrials.gov/ct2/show/NCT01991067).The aim of this prospective study was to characterize the humoral immune response to TBE-vaccination after hematopoietic stem cell transplantation (HSCT). Nineteen adult patients 11 to 13 months after HSCT and 15 age-matched immunocompetent adults received up to three TBE-vaccinations. Antibodies against TBE virus were measured by neutralization test (NT). As primary endpoint, the antibody response (NT-titer of ≥10 and at least a 2-fold increase from baseline 4 weeks after 2nd vaccination) was compared between patients and controls using Fisher exact test. Prior vaccination, 15 (79%) HSCT patients still had detectable neutralizing antibodies. At primary endpoint, the antibody response was significantly lower in patients than in controls (35% versus 93%; p<0.001). The CD4+-cell count was a predictor for an antibody response in patients (p=0.019). Interestingly, the majority of HSCT patients still had detectable antibodies prior vaccination. Following vaccination, antibody response in HSCT patients was associated with the CD4+-cell count.