We examined the male-female collaboration practices of all internationally visible Polish university professors (N = 25,463) based on their Scopus-indexed publications from 2009–2018 (158,743 journal articles). We merged a national registry of 99,935 scientists with the Scopus publication database, using probabilistic and deterministic record linkage. Our database (“The Polish Science Observatory”) included all professors with at least a doctoral degree employed in 85 researchinvolved universities. We determined an “individual publication portfolio” for every professor. The gender homophily principle (publishing predominantly with scientists of the same sex) was found to apply to male scientists — but not to females. The majority of male scientists collaborate solely with males; most female scientists, in contrast, do not collaborate with females at all. Gender homophily in research-intensive institutions proved stronger for males than for females. Finally, we used a multi-dimensional fractional logit regression model to estimate the impact of gender and other individual-level and institutional-level independent variables on gender homophily in research collaboration.