ABSTRACT: BACKGROUND: Several measures have been implemented at international level to ensure that there is a greater focus on sex differences in health research. This study evaluates the effect of various formal incentives that were introduced by a Dutch financer of health research to encourage applicants to include sex differences in research proposals. METHODS: We sampled 213 health research proposals submitted in 2003 to the programmes Prevention (N = 104) and Innovation (N = 109) by the Netherlands Organization for Health Research and Development (ZonMw). These proposals were analysed and categorized with regard to the expressed intention to take sex differences into consideration. Furthermore, those proposals in which such intention was absent were appraised by researchers to determine whether an intention of this kind would have been relevant. RESULTS: We found that 23 % of proposals submitted to Prevention (incentive: programme specific instructions) and 10% of those submitted to Innovation (general set of guidelines) took account of sex differences (difference 13%; 95% CI: 3.1-22.9). Conversely, 66% of the research proposals in Prevention, and 20% in Innovation, failed to take sex differences into consideration, even though this might well have been relevant. CONCLUSION: There is still insufficient incentive for those submitting research proposals to ZonMw to systematically incorporate sex differences when drafting such documents. The provisions in ZonMw's policy need to be amended and better monitored. For this, we formulated some recommendations.