Cardiovascular (CVD) risk factors are under the influence of environmental and genetic factors. Human upstream transcription factor 1 gene (USF1) encodes for a transcription factor, which modulates the expression of genes involved in lipid and carbohydrate metabolic pathways. The aim of this study was to test the hypothesis that USF1 gene variants are associated with CVD risk factors in the Quebec Family Study (QFS). USF1 has been sequenced in 20 QFS subjects with high plasma apolipoprotein B100 (APOB) levels (>1.14 g/l) and small, dense low-density lipoprotein (LDL) particles (> or =250.7 Angstroms and < or =255.9 Angstroms), as well as in five subjects with larger LDL particles. Ten variants were identified in non-coding regions of USF1. Two of these polymorphisms (intron 7 c.561-100 G>A, and exon 11 c.*187 C>T) as well as the c.-56 A>G polymorphism, were genotyped and analyzed in 760 subjects from QFS. Association studies showed that women with c.561-100 A/A and c.*187 T/T genotypes had more favorable adiposity indices (<0.04). In summary, significant associations between relatively common USF1 genetic variants and CVD risk factors were observed in French Canadians.