Prospective population-based surveillance to assess the epidemiology of invasive pneumococcal disease (IPD) in hematopoietic stem cell transplant (HSCT) patients is limited and a comparison to the general population is lacking. By using a population-based Invasive Bacterial Diseases Network surveillance program, we studied the incidence, clinical significance, serotypes and antimicrobial resistance of IPD in a large cohort of adult HSCT patients and the general population. Streptococcus pneumoniae isolates and patient data were collected prospectively from 1995 to 2004. We identified 14 cases of IPD (based on sterile site isolates) in our HSCT population over a 10-year period. This translated to an incidence rate of 347 infections per 100 000 persons per year. This compared to an incidence of 11.5 per 100 000 persons per year in the general population (regression ratio=30.2; 95% confidence interval (CI) 17.8-50.8, P<0.00001). If nonsterile site isolates (respiratory tract) were included, the incidence rate in transplant patients was 446 per 100 000 persons per year. Serotypes 23F and 6B were most common; 100 and 69.2% of isolates were a serotype included in the pneumococcal polysaccharide and conjugate vaccines, respectively. The antimicrobial resistance rates were high, especially for trimethoprim/sulfamethoxazole. HSCT recipients are at significantly greater risk for IPD than the general population. Preventative strategies are necessary.