A patient developed Candida albicans endocarditis and fungemia after undergoing aortic valve replacement with an allograft. The allograft had been found during tissue bank processing to be contaminated with C. albicans, but it was culture-negative for C. albicans after routine disinfection with an antifungal-containing antimicrobial solution. Comparison of the preimplantation and postimplantation C. albicans isolates revealed remarkable genetic similarity, but antifungal susceptibility testing showed that the postimplantation isolate was more resistant to fluconazole and amphotericin B than the preimplantation isolate, suggesting emergence of resistance after disinfection. Implantation of a contaminated heart valve allograft can occur despite disinfection during processing and can result in endocarditis in the recipient. Antimicrobial disinfection protocols that include antifungal drugs may be ineffective. Current U.S. Food and Drug Administration regulations do not require companies to specify details concerning allograft processing. Additional measures may be required to prevent tissue bank release of allografts contaminated with C. albicans or other pathogens.