In order to increase scientific rigor and reproducibility, Drs. Collins (Director, NIH) and Clayton (Director, Office of Research on Women’s Health) spearheaded an effort to require preclinical scientists to consider sex differences in their research [1]. A similar policy addressing the inclusion of women in clinical research has been in effect since 1993 [2]. Researchers are now working towards identifying how best to operationalize these policy initiatives across disciplines and disorders (e.g., [3–6]). The goal of this commentary is to raise awareness and discussion about how to best consider and evaluate possible sex effects in the context of large-scale human genetic studies. In particular, given the current rapid decline in whole genome sequencing costs, the relative affordability of high-throughput genotyping arrays, the establishment of large publicly available datasets and ongoing efforts of international consortia, the time is right to begin including sex as an important variable of interest.