Stearoyl-CoA desaturase 1 (SCD1) activity, a key regulator of lipid metabolism, may be associated with the development of metabolic syndrome (MetS). We examined the association of genetic variation in the SCD1 gene with the occurrence of MetS and its five components in a population of Costa Rican adults (n = 2152; mean age, 58 y; range, 18-86 y). Associations of tag single nucleotide polymorphisms (tagSNP) of the SCD1 gene with prevalence of MetS and its five components were analyzed by use of log-Poisson models with robust variance estimates and linear regression models, respectively. The likelihood ratio was used to test potential gene-fatty acid interactive effects with adipose tissue alpha-linolenic acid. One tagSNP (rs1502593) was significantly associated with an increased prevalence of MetS in the total study sample. Compared with the common homozygous CC genotype, the CT and TT genotypes for rs1502593 were associated with higher prevalence ratios (PR) of MetS for CT vs. CC: [PR = 1.22 (95% CI = 1.03, 1.44)] and for TT vs. CC [PR = 1.24 (95% CI = 1.01, 1.52)]. Among women, we observed borderline positive associations between systolic blood pressure and fasting blood sugar levels and rs1502593 (P = 0.05 and 0.06). Compared to the common haplotype (frequency >/= 5%) with no minor alleles of SCD1 tagSNP, the other two observed common haplotypes carrying the rs1502593 minor allele were significantly associated with elevated prevalence of MetS. No gene-fatty acid interactive effects were observed. Our results suggest that genetic variation in the SCD1 gene may play a role in the development of MetS.