The metabolomic profile of a biofluid can be altered by dietary intake, exercise and disease processes and, thus provides an important tool for the study of many physiological processes. However, in addition to perturbation due to disease, the metabolomic profile of urine and plasma has also been shown to vary due to many intrinsic physiological factors such as age, sex, hormonal status and diurnal variation. Characterisation of this normal degree of variation in the metabolomic profiles of human biofluids is a necessary and important step in the development of metabolomics for use in nutrition-related research. The current review focuses on the impact of sex on the metabolomic profile. A number of studies have reported that sex impacts metabolites such as amino acids, lipids, sugars and keto acids. Furthermore, we examine the effect of the menstrual cycle on the metabolomic profile. Responses to dietary interventions can also differ between the sexes and highlighting this is important for the development of the field of precision nutrition.