Background For winter 2003/2004 in Scotland, it was recommended that all those aged 65 and over be eligible to receive 23-valent polysaccharide pneumococcal vaccine (23vPPV), which has been shown to be effective in reducing the risk of invasive pneumococcal disease (IPD). We assessed the success of the vaccination programme by examining the age specific incidence rates of IPD compared to four previous winter seasons and estimating vaccination effectiveness. Methods Winter season incidence rates of IPD for vaccine targeted (65 years and over) and non-targeted (0-4, 5-34, 35-49, 50-64) age bands were examined for the Scottish population in a retrospective cohort design for winter 2003/2004. Details of all IPD cases were obtained from the central reference laboratory and population vaccine uptake information was estimated from a GP sentinel practice network. Based on the preceding four winter seasons, standardised incidence ratios (SIR) for invasive pneumococcal disease were determined by age-band and sex during winter 2003/2004. Vaccination effectiveness (VE) was estimated using both screening and indirect cohort methods. Numbers needed to vaccinate were derived from VE results using equivalent annual incidence estimates for winter 2003/2004. Results Overall vaccination effectiveness using the screening method (adjusted for age and sex) in those aged 65 and over was 61.7% (95%CI: 45.1, 73.2) which corresponded to a number needed to vaccinate of 5206 (95%CI: 4388, 7122) per IPD case prevented. Estimated effectiveness for the same age group using the indirect cohort method was not significant at 51% (95%CI: -278, 94). Reductions in the winter season incidence rate of IPD were highly significant for all those aged 75+: males SIR=58.8 (95%CI: 41.6, 80.8); females SIR=70.0 (95%CI: 55.1, 87.8). In the 65-74 years age-group, the reduction for females was significant: SIR=60.3 (95%CI: 39.3, 88.4), but not for males: SIR=74.8 (95%CI: 50.8, 106.3). There was no significant protective effect on mortality. Conclusions The introduction of 23vPPV for those aged 65 and over in Scotland during winter 2003/2004, was accompanied with a reduction of around one third in the incidence of IPD in this age group. Vaccination effectiveness estimates were comparable with those from other developed countries.