Abstract. The purpose of this study was to analyse the effect of the T-786C polymorphism and intron 4 27 bp variable number tandem repeat(VNTR) eNOS markers for their potential association with Systemic Lupus Erythematosus(SLE), Hashimotos thyroiditis(HT) and Rheumatoid arthritis(RA) as well as to explore their effect on eNOS mRNA expression and nitrate production (NOx). Kuwaitis (n = 383) matched by age, gender and ethnicity were genotyped by fluorescent-labelled-restriction fragment length polymorphism (RFLP) and fragment analysis. Expression of eNOS mRNA was analysed using RT-PCR and sera from subjects were screened for NOx using ELISA. Analysis of the allelic frequency revealed a significant association of the 4b allele with susceptibility to SLE (p = 0.0092, OR = 1.76). The 4bb genotype was found to be associated with SLE (p = 0.0076, OR = 1.97) and HT (p = 0.05, OR = 1.81). Allelic and genotypic distribution did not differ between RA patients and healthy control subjects. The 4bb genotype resulted in reduced expression of eNOS mRNA in SLE, RA and HT, but only the reduction in HT was significant (p = 0.05). The 4ab genotype revealed a significant association with increased eNOS expression in HT (p = 0.03) and RA (p = 0.014) patients, and elevated NOx levels were detected in the autoimmune disease cohorts (p < 0.05) when compared to healthy control subjects. The T-786C SNP failed to show a significant association (p > 0.05) with SLE, HT, and RA patients. This study is the first to reveal a significant association between the 4bb genotype of the 27 bp VNTR and susceptibility to HT. The expression of eNOS is related to the number of 27 bp repeats, with heterozygous 4bb repeats showing a decrease in eNOS expression. eNOS -endothelial nitric oxide synthase.