A survey of the coverage, distribution and the factors associated with use of influenza and pneumococcal vaccines among general practitioners (GPs) in primary care and in hospital settings was carried out in 53 general practices in Scotland taking part in the ‘Continuous Morbidity Recording’ (CMR) programme. The annual vaccine distribution increased substantially among 53 general practices from 1993 to 1999 and in Scotland as a whole from 1984 to 1999. From the questionnaire, overall coverage was 43% (95% CI 38–48) for influenza vaccine in the 2000–1 season and 13% (95% CI 9–16) for pneumococcal vaccine in the last 5 year period, in high-risk patients recommended for these vaccines by the Department of Health (DoH). Influenza vaccine coverage was highest in the elderly (65 years of age and above) at 62% (95% CI 59–74). Although pneumococcal vaccination is not currently recommended for all elderly, coverage of this vaccine was also higher in this group (22%, 95% CI 16–29). In the majority of patients (influenza vaccine, 98% and pneumococcal vaccine, 94%), vaccination was carried out in general practice. Only 2% of patients had received pneumococcal vaccination in a hospital setting. The level of influenza and pneumococcal vaccination varied with the level of deprivation. Most GPs considered that the responsibility for influenza and pneumococcal vaccination lay with them. Forty-five percent of GPs reported having a written policy with set target for influenza vaccination and 11% for pneumococcal vaccination.