WOKW rats develop a complete metabolic syndrome closely resembling human disease. Since genetic studies using male (WOKW x DA)FB progeny showed that several independent genetic factors were involved, a polygenic basis for the syndrome in WOKW was assumed. However, because the metabolic syndrome in human clearly demonstrates sex differences, we have extended our study to include both male and female (WOKW x DA)FS progeny in a genome-wide scan. Male- or female-specific quantitative trait loci (QTLs) were mapped for body weight, body mass index, adiposity index and serum insulin on chromosomes 1 and 5, serum triglycerides on chromosomes 4, 7, 11, and 16, serum total and high density lipoprotein cholesterol on chromosomes 3, 4, 5, 10, and 17, and serum leptin on chromosomes 8 and 16 as well as blood glucose and glucose tolerance (AUC) on chromosomes 3, 4 and 17. QTLs for both, males and females were only found for body weight on chromosome 1 and for serum total cholesterol on chromosome 3 and 10. These findings clearly demonstrate that there are sex-specific and sex-independent QTLs for facets of the metabolic syndrome in WOKW rats.