This study aimed at characterizing the fatty acid (FA) composition of red blood cell (RBC) phospholipids in children and adolescents with primary hyperlipidemia, and to ascertain potential association with serum lipid profile and dietary factors. At this purpose, 54 probands aged 6-17 years were recruited. Subjects showed a low omega-3 index (eicosapentaenoic acid, EPA+docosahexaenoic acid, DHA < 4%). Compared to males, females had a trend toward lower levels of total monounsaturated fatty acids (MUFA) and MUFA/saturated fatty acids (SFAs) ratio in RBCs. An inverse relationship between MUFA concentration in RBCs and serum cholesterol or HDL-C/triglycerides ratio was found. Omega-6 polyunsaturated fatty acids (n-6 PUFA) were positively associated to serum HDL-C levels, and inversely to dietary cholesterol. Fiber intake was positively associated with MUFA/SFA ratio. In conclusion, we provide the first experimental data on phospholipid FA composition of RBCs in hyperlipidemic children, showing sex differences and an overall low omega 3-index.