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The under-representation of women in science and technology is a matter of current great concern. Obtaining patent-based indicators by gender is crucial to analyse the situation of women in innovation, identify potential cases of gender inequalities, and support policy measures to promote gender balance. In this article we analyse men and women involvement in Spanish patents applied to the European Patent Office during 1990–2004. At least one female inventor is present in 18% of the patents; female contribution amounts to 9% of the total and 14% of inventors are women. Female involvement is above average in the academic public sector and in specific thematic areas, while the share of women in industry is very low. Female inventors show a stronger trend to collaborate than their male counterparts, as measured through their lower percentage of single-inventor patents and their higher co-inventorship index. Over the 15-year period under analysis, women’s involvement in patenting activity shows an upward trend, especially at universities and in cross-gender teams and the specialization profile of women tends to expand. Main difficulties in the development of patent-based indicators by gender are pointed out and the relevance of indicators to monitor the situation of women in innovation activity is highlighted. [ABSTRACT FROM PUBLISHER]