This exploratory trial evaluates the effect of a structured exercise (STEX) or lifestyle intervention (PASS) program upon cardiovascular (CV) disease risk factors in children. Sixty-one schoolchildren were randomly assigned by school to an intervention or control (CON) condition. The effect of the STEX (compared with CON) was a mean benefit of -0.018 mm for average maximum carotid intima-media thickness. The PASS intervention did not result in clinically important effects, and no other substantial changes were observed. Relatively high probability of clinically beneficial effects of the STEX intervention suggests that a larger, definitive randomized trial with longer follow-up is warranted.