“Research collaboration” and “women in science” have been widely studied for half a century. However, the gender context of academic science has changed substantially, with more female scientists entering the higher education sector every decade and increasingly occupying high academic positions. Our story is about man-woman collaboration in research in this changing context. We examined male-female collaboration practices of all internationally visible (25,000) Polish university professors based on their 160,000 Scopus-indexed publications. We merged a national registry of 100,000 scientists (with full administrative and biographical data) with the Scopus publication database. We examined the propensity to conduct same-sex collaboration across male-dominated, female-dominated, and gender-balanced disciplines. We found out that across all age-groups and all academic positions, the majority of male scientists collaborate solely with males. The majority of female scientists, in contrast, do not collaborate with females at all. So we found out that the gender homophily principle (i.e. publishing predominantly with scientists of the same sex) works powerfully for male scientists – but does not seem to work for female scientists. Having an integrated biographical, administrative, publication, and citation database at our disposal (which we termeded “The Observatory of Polish Science”), we were able to examine the propensity to engage in same-sex collaboration across several new dimensions. This research goes beyond traditional bibliometric studies of gender-based homophily in research collaboration by combining the data routinely inaccessible to large-scale studies (such as the biological age of all scientists, and the stages of their academic careers) and the data routinely accessible in bibliometric studies, such as journal prestige, academic disciplines, and institutional type. We draw conclusions from a single-nation context to academic science in general and discuss practical implications of our research for academic careers.