Background We investigated whether variations in lipoprotein lipase activity, a key post-prandial enzyme involved in the removal of circulating dietary triglycerides, could contribute to the previously described nocturnal lipid intolerance, Methods We studied lipoprotein lipase activity in 12 healthy volunteers (five women, seven men) at 11.30 h and 23.30 h on two separate occasions. Subjects consumed a high-fat mixed meal at 07.30 h for the morning study or 19.30 h for the evening study. Then, after a 4-h fast, subjects were given an intravenous bolus of 7500 U heparin. Blood samples were collected before and 15 min after heparin administration for measurement of lipoprotein lipase, hepatic lipase, triglycerides and non-esterified fatty acids concentrations. Results Post-prandial post-heparin lipoprotein lipase activity was greater in the morning than in the evening (16.5 +/- 1.4 versus 14.4 +/- 1.0 mumol oleate/mL/h; P<0.05). Post-prandial post-heparin hepatic lipase activity was also greater in the morning than in the evening (8.7 +/- 1.5 versus 8.1 +/- 1.6 μmol oleate/mL/h; P=0.002). There were no other significant diurnal differences. Conclusion We report a diurnal variation in post-prandial lipoprotein lipase activity. This is consistent with the notion that decreased nocturnal insulin sensitivity extends to insulin's actions on lipoprotein lipase and provides a possible explanation for nocturnal lipid intolerance.