Background: For the second time a plan to monitor public health and health inequalities in the Netherlands through general practice was put into action: the Second National Survey of General Practice (DNSGP-2, 2001). The first aim of this paper is to describe the general design of DNSGP-2. Secondly, to describe self assessed health inequalities in the Netherlands. Thirdly, to present differences in prevalence of chronic conditions by educational attainment using both self-assessed health and medical records of GPs. Finally, inequalities in 1987 (DNSGP-1) and 2001 will be compared. Methods: Data were collected from 96 (1987) and 104 (2001) general practices. The data include background information on patients collected via a census, approximately 12 000 health interview surveys per time point and more than one million recorded contacts of patients with their GPs in both years. The method of statistical analysis is logistic regression. Results: The analyses shows that the lower educated have significantly higher odds of feeling unhealthy and having chronic conditions in 2001. Diabetes and myocardial infarction (GP data) showed the largest difference in prevalence between educational groups (OR 2.5 and 2.4, self-reported data). The way the data is collected (self-assessment versus GP registration) hardly affects the magnitude of the educational differences in the prevalence of chronic conditions. The pattern of health inequalities across chronic conditions in 1987 and 2001 hardly differs. Diabetes doubled in prevalence and health inequalities were not significant in 1987, but compared to the other conditions were largest in 2001 (OR 1.1 versus 2.5). Conclusion: Health inequalities were shown to be substantial in 2001 and persistent over time. Socio-economic differences were shown to be similar using self-assessed health data and GP data. Hence, a person’s educational attainment did not appear to play a part in presenting health problems to the GP. Key points: † Socio-economic differences showed to be similar using ...