The objective of this study was to investigate the relationship between physical fitness, lipids, and apolipoproteins in a cross-sectional study using a two-stage probability sample of the population of Northern Ireland. The main outcome measures were physical fitness using VO2max estimated by extrapolation from submaximal oxygen uptake while walking on a motor driven treadmill, and total cholesterol, HDL cholesterol, LDL cholesterol, triglycerides, HDL2 and HDL3, and Lp(a). There were no significant relationships with fitness, after adjustment for possible confounders, with the exception of a positive relationship with HDL2 in males (P < or = 0.01) and Lp(a) in females (P < or = 0.05). There was also a relationship between physical fitness and HDL:apo AI ratio in males and females after adjustment for possible confounders (P < or = 0.05). We concluded that there were few relationships between lipid parameters and physical fitness after adjustment for possible confounders. The relationship between physical fitness and Lp(a) in females suggests a benefit associated with physical fitness and the relationship between physical fitness and HDL:apo AI ratio was in keeping with improved HDL cholesterol transport.