Although the share of female PhDs has increased explosively since the 1980s, little research has focused on the utilisation and remuneration of female versus male scientific human capital. Using rich Swedish cross-sectional register data on the stock of PhDs in 2004, this paper analyses to what extent men and women choose academic versus non-academic employment, and to what earnings differences these choices lead. Results show that women are significantly less likely than men to be academically employed in the natural sciences and medicine, whereas no significant gender differences prevail for the social sciences and the humanities. On average, women earn 15 per cent less than men, and the academically employed earn 24 per cent less than PhDs outside academia. Gender earnings differences are larger in the academic than in the non-academic labour market in the humanities and the natural sciences, whereas the opposite holds in the social sciences and medicine.