A great number of stakeholders have a keen interest in issues surrounding sex differences. These participants in the discourse often use the same evidence to draw opposite conclusions, with implications for individuals and society as a whole. One part of the maelstrom and associated emotionality derives from confounds between the concepts of "sex" vs. "gender", even among professionals. Here, the oft-repeated point is made that evidence for gender differences can't be derived from the animal research, once the generally accepted conception of gender as a process unique to humans, is acknowledged. Nevertheless, considered at a more general level, the developmental and epigenetic mechanisms that give rise to differences in behavior among individuals and groups is exquisitely explored in animal studies but relatively poorly in research on humans. The focus on animal research here, starts with the fact that virtually each cell of the body has sex chromosomes (XX and XY), along with the intracellular genetic and cytoplasmic mechanisms associated with circadian (circa-about, dies-day) timing. The consequences of these sex×circadian interactions for physiology and behavior at cellular and higher levels of organization are considered in systems where compelling evidence is available. These include sex differences in the circadian timing system, the hypothalamic-pituitary-adrenal (HPA) axis, and in metabolism. The evidence highlights sex differences in cells throughout the body and thus has implications for higher level processes and systems such as sleep/wake patterns. In a more general sense, they point to mechanisms that could give rise to gender differences. In summary, the viewpoint presented here is that the circadian timing system can be used very elegantly to explore the contributions of genetic and hormonal sex differences on biological systems at many levels.