Subtle gender dynamics in the publishing process involving collaboration, peer-review, readership, citation, and media coverage disadvantage women in academia. In this study we consider whether commenting on published work is also gendered. Using all the comments published over a 16-year period in PNAS (N = 869) and Science (N = 481), we find that there is a gender gap in the authorship of comment letters: women are less likely than men to comment on published academic research. This disparity is greater than gender differences in the publication of research articles. There is also a gendered pattern in commenting: women comment writers are relatively less likely to engage with men's research. If left unaddressed, these patterns in academic commenting could impede scholarly exchange between men and women and further marginalize women within the scientific community.