Owing to the gender-specific disadvantage of women academics in research organisations women should be more forcefully promoted in research programmes. One instrument for achieving equality between women and men is the strategy of gender mainstreaming. Gender mainstreaming in research programmes involves two main dimensions. One concerns the research structures – that is, the equal participation of women and men in research. The other concerns the stimulation of gender-relevant research. Bringing them together, the question arises of how research programmes – in particular the call for applications and selection procedures for research projects – are to be drawn up so that both dimensions are taken into account. The aim of this project was to draw up a guideline for a strategy of gender mainstreaming in interdisciplinary environmental research programmes. This included the objectives of combining previous experience and further development of the implementation of gender mainstreaming for research programmes, a proposal of measures for promoting equality within research programmes and a proposal of measures for implementing gender mainstreaming in calls for applications and application procedures for research programmes.