The epidemiology of herpes zoster (HZ) in contemporary autologous hematopoietic cell transplant (HCT) recipients, and the impact of acyclovir/valacyclovir (ACV/VACV) prophylaxis, is not well described. In this observational study from 2002–2010, we retrospectively identified 1,000 varicella zoster virus (VZV) seropositive autologous HCT recipients with up to five years of follow up. The incidence of HZ and use of ACV/VACV prophylaxis were determined through review of medical records and mailed questionnaires. Risk factors for HZ were determined by multivariable Cox regression. Over a period of five years post-autologous HCT, 194 patients developed at least one HZ episode with a cumulative incidence of 21%; 159/194 (82%) were not on prophylaxis at the time of HZ. A second episode of HZ occurred in 31/194 (16%) patients. Patients taking ACV/VACV had reduced risk for HZ (adjusted hazard ratio [aHR], 0.59; 95% CI, 0.37–0.91), whereas those older than the median age (≥55.5 years) had increased risk (aHR 1.42, 95% CI 1.05–1.9). Disseminated VZV was reported in 8% and post-herpetic neuralgia in 13% of patients. We demonstrate a high burden of HZ late after autologous HCT, despite long-term antiviral prophylaxis. Improved prevention strategies are needed to provide sustained protection against HZ after autologous HCT.