Background: Potential risks for transfusion-transmissible infections are identified by donor history questionnaires (DHQs), and donors with higher risks are deferred from donation. We assessed to which extent the currently used DHQs support the identification of infections among blood donors. Methods: Between 2006 and 2013, we analyzed data from notified HIV and HCV cases in the general population and positive blood donors in Germany. Logistic regressions were used to identify relevant infection risks. We estimated the possible effect of improved capture of risk factors for donor selection by calculation of population attributable fractions (PAF). Results: Risky sexual contacts - MSM as well as heterosexual contacts - were the most prominent infection risks among HIV-infected donors. Whereas MSM contacts were significantly less reported by donors than by cases from the general population, 58% of donors disclosed heterosexual risks compared to 26% of notified cases. The complete identification of heterosexual risk contacts might prevent acceptance of 53% of HIV-infected donors. HCV-infected donors were more likely to report heterosexual exposure, imprisonment, and piercing/tattoo than notified HCV cases. Improved recording of piercing/tattoo could prevent acceptance of 16% of HCV-infected donors. Conclusion: Donor selection should be improved with special attention to the identification of (hetero)sexual risk factors, invasive procedures (piercing/tattoo and imprisonment) applying well-designed DHQs, effective donor education, and confidential environment in all steps of the selection process.