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The biological differences between males and females encompass different sex chromosomes and differing sex hormones. These differences contribute to sex differences in the development of disease. Typical examples are the higher prevalence of non-reproductive cancers in males, and the higher prevalence of auto-immunity in females. Another example are the sex differences in cardiovascular diseases driven by atherosclerosis. Despite the differences in atherosclerosis in which females develop more often stable plaques as compared to males with more unstable plaques, we lack knowledge about female biology in atherosclerosis. This is because the majority of biomedical research has been performed in male patients, male animals, and male cells. Using a systematic review, we show that sex stratification is scarce in cardiovascular epigenetics. Next, we determined how sex influenced gene regulation by integrating DNA methylation and RNA-sequencing data of the atherosclerotic plaque. The sex differential genes suggest that smooth muscle cells in the plaque are heavily subject to sex differences as underlined by deconvolution analyses, regulatory linkage, RNA-sequencing and single-cell RNA-sequencing. Systems biology approaches have been successfully used to find novel disease targets, such as for coronary artery disease. However, these studies also mainly use predominantly male populations. We generated sex-specific gene regulatory networks of atherosclerosis and determined that female key drivers of atherosclerosis are involved in smooth muscle cell phenotype switching, as compared to the more immune system biology from male samples. It shows that completely different biology erupts when we study male and female tissues separately, but in equal numbers. Male biology in atherosclerosis seems to center around inflammation, whereas female biology seems to converge on the smooth muscle cell. To determine whether sex differences exist within cell types, we generated RNA-sequencing data from endothelial cells from new-born twins and adults. We found that genes that are differentially expressed between the sexes at birth and in the adult stage are enriched for coronary artery disease genes. Many biological sex differences are described also in healthy tissue from different organs all over the human body, since a body-wide analysis on 24 tissues in this thesis found that the gene activity of 20.1% of the 13,787 studies genes are affected by sex. We may also use information generated from sex-specific diseases and risk factors to detect novel biology that may be important for both sexes, for example, we used RNA-sequencing data of platelets of women with former preeclampsia to detect biology important for accelerated atherosclerosis that may inform about processes in men as well. Lastly, we postulate conjectures about sex chromosomal genes and how these may influence sex-bias in disease, and conclude that attention to sex chromosomal genes is warranted. This dissertation shows that sex is an important player in cardiovascular health and disease, in which sex affects the genetic material and the regulation thereof in multiple ways. By studying sex differences standardly, we discover biology that until now has remained hidden in all the biology based on males. This knowledge may contribute to new findings important for both males and females.