Recent data suggest that subclinical atherosclerosis is more related to visceral adipose tissue distribution than to overall fat mass. Both perirenal fat and epicardial fat are visceral fat depots surrounding the kidneys and the myocardium, respectively, which can be easily assessed by ultrasound. Their clinical relevance in children is largely unknown. This review describes studies relating perirenal and epicardial fat to cardiovascular disease or carotid intima-media thickness (cIMT), a well-established surrogate for subclinical atherosclerosis, and discusses this in context with our own data from children. In adults, both perirenal and epicardial fat are useful biological markers of visceral obesity. The former has been related to hypertension in overweight subjects and with atherosclerosis in patients with human immunodeficiency virus. The latter was associated with several metabolic syndrome components and with calcification of the carotid artery. In healthy prepubertal children, both epicardial and perirenal fat thickness, rather than total body fat mass, were related to cIMT. Ultrasonography measures of perirenal and epicardial fat are related to atherosclerosis in adults and may be convenient tools for the assessment of cardiometabolic risk in children.