The aim of this study was to assess any association between an Xmn1 restriction site polymorphism of the apo Al gene and lipoprotein levels in obesity. A cross sectional study was made of lipid variables in relation to genetic and anthropometric factors in obese people at the Nutrition Outpatient Clinic of Bichat Hospital in Paris, France. The subjects were 97 unrelated French Caucasian subjects (65 women and 32 men) selected on the basis of 20% overweight. The following main outcome measures were recorded: body mass index (BMI) and waist to hip ratio (WHR), cholesterol (C) and triglyceride (TG) concentrations in serum and lipoproteins (including HDL subfractions), apolipoproteins Al and a, determination of apo AI Xmn1 genotypes. Three alleles, designated X1, X2, X3, could be detected with frequencies 0.84, 0.12, and 0.04 respectively. The X2 carriers had higher concentrations of LpA-I, A-II (HDL particles containing both Apo Al and Apo AII) in the whole group: 0.90 vs 0.77 and 0.72 g/l in X1X1 and X1X3 respectively (P < 0.01). The genotype X1X2 was also associated with higher HDL-C in obese men (0.47 vs 0.36 g/l in X1X1, P < 0.05). In X1X1 women, BMI was positively correlated with serum and VLDL-TG (P < 0.05) and negatively with HDL(2)-C (P < 0.05), WHR being positively correlated with serum TG (P < 0.05), VLDL-TG (P < 0.01) and negatively with HDL-(P < 0.05) and HDL(2)-C (P < 0.01). These correlations were not found in subjects carrying the X2 allele. In subjects with at least one X2 allele, Apo AI levels were positively correlated with the WHR (P < 0.05). This result could be explained by the correlation between Lp A-I, A-II and WHR. These results suggest a modulator role on lipid metabolism of a region close to the apo AI Xmn1 RFLP locus in obese people.