The aim was to determine whether blood glucose or cholesterol is the more prominent contributor to cardiovascular dysfunction in 101 African men and 99 African women. We measured ambulatory daytime blood pressure (BP), carotid intima-media thickness (CIMT), and determined blood glucose and lipids in serum. High-density lipoprotein cholesterol (HDL) (p = 0.002) and HDL: total cholesterol (HDL:TC) (p ≤ 0.001) were significantly lower, while serum glucose (p ≤ 0.001) was significantly higher in men. In single, partial, and multiple regression analysis, BP correlated positively with blood glucose in men. Furthermore, CIMT (B = −0.50; p = 0.009) correlated negatively with HDL:TC in men. While in women CIMT (B = 0.346; p = 0.015) correlated positively with glucose. In conclusion, subclinical atherosclerosis is significantly related to an unfavorable HDL profile in men, whereas in women, this link is stronger with fasting glucose.