Polynesian individuals are leaner with greater musculature than Caucasians of an equivalent size, and this genetically different morphology provides a physique that is often compatible with success in a number of sports, including rugby union. Evidence indicates that Polynesians have greater stores of absolute and relative abdominal fat mass and this is known to confer cardiometabolic risk. The aims of this study were to (1) explore the relationship between ethnicity, visceral adipose tissue (VAT), and cardiometabolic disease risk markers in elite Caucasian and Polynesian rugby union athletes, and (2) assess the impact of a pre-season training programme on these markers. Twenty-two professional rugby union athletes of Caucasian (n = 11) and Polynesian (n = 11) descent underwent physique assessment via surface anthropometry, dual-energy X-ray absorptiometry, and magnetic resonance imaging before and after an 11-week pre-season. A fasted blood test was undertaken at both time points. Compared to Caucasians, at baseline Polynesians displayed significantly higher VAT (771 ± 609 cm3 vs 424 ± 235 cm3; p = 0.043), triglycerides (1.0 ± 0.9 mmol/L vs 0.6 ± 0.2 mmol/L; p = 0.050), and low-density lipoprotein cholesterol (3.1 ± 0.9 mmol/L vs 2.3 ± 0.7 mmol/L; p = 0.019). Similar changes were observed in both groups over the pre-season period in VAT and blood biochemical markers. Polynesian rugby union athletes were more likely than Caucasians to exhibit risk factors associated with cardiometabolic disease, such as elevated VAT and unfavourable lipid profiles. Further longitudinal research is required to identify and explain the short- and long-term risk of cardiometabolic disease in athletes of Polynesian descent.