A number of studies suggest that scientific papers with women in leading-author positions attract fewer citations than those with men in leading-author positions. We report the results of a matched case-control study of 1,269,542 papers in selected areas of medicine published between 2008 and 2014. We find that papers with female authors are, on average, cited between 6.5 and 12.6% less than papers with male authors. However, the standardized mean differences are very small, and the percentage overlaps between the distributions for male and female authors are extensive. Adjusting for self-citations, number of authors, international collaboration and journal prestige, we find near-identical per-paper citation impact for women and men in first and last author positions, with self-citations and journal prestige accounting for most of the small average differences. Our study demonstrates the importance of focusing greater attention on within-group variability and between-group overlap of distributions when interpreting and reporting results of gender-based comparisons of citation impact.