We analyzed the impact of a requirement introduced in December 2010 that all applicants to the Canadian Institutes of Health Research indicate whether their research designs accounted for sex or gender. We aimed to inform research policy by understanding the extent to which applicants across health research disciplines accounted for sex and gender. We conducted a descriptive statistical analysis to identify trends in application data from three research funding competitions (December 2010, June 2011, and December 2011) (N = 1459). We also conducted a qualitative thematic analysis of applicants' responses. Here we show that the proportion of applicants responding affirmatively to the questions on sex and gender increased over time (48% in December 2011, compared to 26% in December 2010). Biomedical researchers were least likely to report accounting for sex and gender. Analysis by discipline-specific peer review panel showed variation in the likelihood that a given panel will fund grants with a stated focus on sex or gender. These findings suggest that mandatory questions are one way of encouraging the uptake of sex and gender in health research, yet there remain persistent disparities across disciplines. These disparities represent opportunities for policy intervention by health research funders.