Aim To investigate the association between Fractalkine receptor CX3CR1 gene 249V/I polymorphism and early-onset coronary artery disease （CAD） and lipid ratios in patients with no classic risk fators. Methods By polymerase chain reaction and restriction fragment length polymorphism （PCR-RFLP）, we examined the frequencies of V249I among early-onset CAD patients （n149 ＜50 years）, late-onset CAD patients （n150 ＞65 years） and healthy controls （n149, 47～93 years） without known CAD risk factors. We compared plasma total cholesterol （TC）/high density lipoprotein cholesterol （HDLC） ratio and apolipoprotein B （ApoB）/apolipoprotein A1 （ApoA1） ratio among the groups and mutation carriers and non-carriers. Results There were significant differences in 249V/I allele frequencies among the three groups （P<0.0001）. TC/HDLC and ApoB/ApoA1 ratios were significantly higher in early-onset CAD patients compared with late-onset CAD patients and healthy controls （P<0.0001） and independent on either mutation. Conclusions The I249 allele of the Fractalkine receptor CX3CR1 gene may be associated with the age of patients with CAD. We also found an independent association between high lipid ratios and the age of patients with CAD.