Abstract Background Cross-country comparisons of unofficial payments in the health sector are sparse. In 2002 we conducted a social audit of the health sector of the three Baltic States. Methods Some 10,320 household interviews from a stratified, last-stage-random, sample of 30 clusters per country, together with institutional reviews, produced preliminary results. Separate focus groups of service users, nurses and doctors interpreted these findings. Stakeholder workshops in each country discussed the survey and focus group results. Results Nearly one half of the respondents did not consider unofficial payments to health workers to be corruption, yet one half (Estonia 43%, Latvia 45%, Lithuania 64%) thought the level of corruption in government health services was high. Very few (Estonia 1%, Latvia 3%, Lithuania 8%) admitted to making unofficial payments in their last contact with the services. Around 14% of household members across the three countries gave gifts in their last contact with government services. Conclusion This social audit allowed comparison of perceptions, attitudes and experience regarding unofficial payments in the health services of the three Baltic States. Estonia showed least corruption. Latvia was in the middle. Lithuania evidenced the most unofficial payments, the greatest mistrust towards the system. These findings can serve as a baseline for interventions, and to compare each country's approach to health service reform in relation to unofficial payments.