This study examines missed opportunities for recommended influenza vaccine and 23-valent pneumococcal vaccine (23vPPV) among hospitalised elderly persons. 4772 inpatients aged > or = 65 years (cases of pneumonia and frequency-matched randomly selected cohort subjects) participated from two large tertiary Australian hospitals. For subjects unvaccinated with influenza vaccine (past year), 1110/1115 (99.6%) had visited either a doctor (99.4%, mean 11.2 visits) or the same hospital (52.0%, mean 1.5 visits). For those unvaccinated with 23vPPV (past 5 years), 1809/1813 (99.8%) had visited either a doctor (99.7%, mean 11.2 visits) or the same hospital (51.5%, mean 1.5 times) in the past year; 71% had been admitted to the same hospital in the past 5 years (mean 3.4 times). 2.3% of all subjects had vaccination status recorded. No unvaccinated subject was vaccinated during admission, despite approximately 40% reporting acceptability of vaccination if offered. Previous hospitalisation was a risk factor for being unvaccinated. Barriers to implementation of current vaccination policy in the hospital setting require formal evaluation in Australia.