Some studies have demonstrated that genetic variance of apolipoprotein B (APOB) plays an important role in lipid metabolism in childhood. However, little information exists about the distribution and effect of the APOB polymorphism among the population from Guangxi, where populations have developed through complex interaction among various ethnic groups over the centuries. The purpose of this study was to investigate the association of genetic polymorphisms at the APOB XbaI, EcoRI and MspI restriction sites with body mass index (BMI), serum protein and lipid profiles in children of Guangxi.Genomic DNA was extracted from 200 healthy children from Guangxi. APOB XbaI, EcoRI and MspI genotypes were determined by PCR-restriction fragment length polymorphism (RFLP) analysis. BMI was evaluated. Fasting serum levels of total protein (TP), albumin (Alb), globulin (Glo), lipoprotein (a) [Lp(a)], total cholesterol (TC), triglyceride (TG), high density lipoprotein cholesterol (HDL-C), low density lipoprotein cholesterol (LDL-C), apolipoprotein A1 (apoA1) and apoB were measured.Subjects with X+ allele exhibited significantly higher BMI, and serum levels of Lp(a), TC, TG, LDL-C and apoB than those with X- allele (p0 0.05).APOB XbaI and EcoRI restriction sites may serve as potential genetic markers affecting BMI, serum protein and lipid profiles in children from Guangxi. Living habits and diet should be modified, according to the genetic polymorphism of APOB. In addition, because the groups of rare allele carriers of XbaI and MspI polymorphisms are very small, the significance of the statistical analysis may be weak.