The aim of this study was to compare the associations between waist circumference (WC) measured at three different sites with total intra-abdominal (visceral) adipose tissue (IAAT) volume and cardiometabolic risk factors. WC was measured above the iliac crest (WCiliac crest), below the lowest rib (WCrib), and midway between both sites (WCmiddle) in a sample of 540 participants aged between 6 and 78 years. In a subgroup of 75 overweight and obese adults, WC measurement sites were analyzed in the context of weight loss. The main finding of this study was that WC had a stronger correlation with subcutaneous adipose tissue (SAT) than with IAAT irrespective of the site of measurement. When comparing different WCs, results showed that WCrib was most specific for IAAT in women. In contrast, the WCiliac crest had a lower association with IAAT, but had the highest relationships with SAT. This is consistent with significantly lower associations between WCiliac crest and cardiometabolic risk factors in women. Thus, WCrib or WCmiddle in women appeared to be better correlated with cardiometabolic risk factors than WCiliac crest. Moreover, only WCrib predicted weight loss associated decreases in IAAT in women. In men, all WC measures showed similar results. In prepubertal and pubertal children, none of the WC measures was consistently better than the other. It was also observed that at any cutoff levels (80 or 94 cm and 88 or 102 cm), men had ~3.8 times more IAAT than women which could partly explain the higher mortality and morbidity associated with the same body mass index in men than in women. Thus, these findings suggest that even though the measurement site of WC is not that critical when looking for the best index of IAAT, WCrib seemed to be a better marker for intra-abdominal fat volume and cardiometabolic risk factors in both sex. More studies are needed to determine specific cutoffs for WCrib.