The aim of this study was to compare HDL-cholesterol and triglyceride levels in patients with familial hypercholesterolemia (FH) with a representative sample of the Czech population. For the FH group: data of 1728 adult patients with FH (600 males and 1128 females) were taken from the MedPed CR database. The control group were 1995 individuals of the population sample of the Czech post-MONICA study (956 males and 1039 females). Compared with controls, FH males showed higher levels of HDL-cholesterol and triglycerides. After adjustment for age and BMI, the increase in triglycerides remained significant in the subgroup of non-FDB males only. Compared with controls, HDL-cholesterol was lower, while triglycerides were higher in FH females. After adjustment for age and BMI, HDL-cholesterol remained lower in the subgroup of FH females without FDB whereas triglycerides were higher in both female subgroups. A lower HDL-C in the group of FH patients compared with control subjects was demonstrated in FH females without FDB only. Elevated triglyceride levels were found in FH males and females, except for males with FDB.