Women and men store lipid differently within the body with men storing more fat in the android region and women storing more fat in the gynoid region. Fat is predominately stored in adipose tissue as triacylglycerides (TG); however, TG are also stored in other tissues including the liver and skeletal muscle. Excess hepatic TG storage, defined as a TG concentration >5% of liver weight and known as nonalcoholic fatty liver disease (NAFLD), is related to the metabolic syndrome. Similarly, elevated skeletal muscle TG, termed intramyocellular lipids (IMCL), are related to insulin resistance in obesity and type II diabetes. Men store more hepatic TG than women and, unsurprisingly, NAFLD is more prevalent in men than women. Women store more IMCL than men, yet type II diabetes risk is not greater, which is likely due to the manner in which women store TG within muscle. Sex-based differences in TG storage between men and women are underpinned by differences in messenger RNA expression, protein content, and enzyme activities of skeletal muscle and hepatic lipid metabolic pathways. Furthermore, women have a greater reliance on lipid during exercise because of upregulation of lipid oxidative pathways. The purpose of this review is to discuss the role of sex in mediating lipid storage and metabolism within skeletal muscle and the liver at rest and during exercise and its relationship with metabolic disease.