Decreased adiponectin level, the adipose tissues hormone, is related to high body mass and insulin resistance, which are risk factors for atherosclerosis. It was shown, that cigarette smoking and high homocysteine (Hcy) level are associated with low level of adiponectin. In the presented study we search for the associations between 5 polymorphisms in genes involved in Hcy metabolism - methylenetetrahydrofolate reductase (MTHFR) and paraoxonase 1 (PON1), smoking, adiponectin levels and insulin resistance in subjects with coronary artery disease (CAD). The studied group consisted of 152 patients subjected to coronary arteriography. In 116 patients significant atherosclerotic changes in vascular vessels were confirmed (CAD group), remaining patients were considered as the control group. In studied group, the levels of glucose, insulin, adiponectin and blood lipids profile were measured. Adiponectin and insulin levels were determined by radioimmunological assays. The insulin resistance was calculated using mathematical HOMA model. MTHFR 677C>T, 1298A>C, PON1 -108C>T, L55M, Q192R polymorphisms were ascertained by PCR-RFLP methods. In the studied group (N = 152), significantly decreased adiponectin levels and higher degree of insulin resistance were present in subjects with angina pectoris (N = 129) and peripheral atherosclerosis (N = 32), whereas in the cases of CAD, confirmed in coronary arteriography (N = 116), only the higher degree of insulin resistance was noted. Arterial hypertension (p = 0.004), diabetes mellitus (p = 0.03) and smoking (p = 0.04) were the most significant vascular risk factors associated with the low adiponectin levels. In CAD group, negative correlations between the level of adiponectin and the dose of MTHFR 677T (r = - 0.238; p < 0.05) and PON1 55M (r = -0.251; p < 0.05 alleles were found. The MTHFR 677T allele was also correlated with degree of insulin resistance (r = 0.391; p < 0.05). In smokers, these genetic associations were stronger (r = -0.394; = -0.353; r = 0.440; respectively), which demonstrates, that the negative effects of MTHFR 677T and PON1 55M alleles are enhanced by smoking. Moreover, only in smokers the correlations between adiponectin levels and: the degree of insulin resistance (r = -0.465; p < 0.01) and the levels of HDLC (r = 0.479; p < 0.01) were seen. In summary, in CAD patients, particularly in smokers, occurrence of MTHFR and PON1 risk alleles is associated with the decreased adiponectin levels and/or increased degree of insulin resistance.