Peroxisome proliferator activated receptor-gamma is an important factor in adipocyte differentiation and energy metabolism and is thus a candidate gene for obesity, insulin resistance and dyslipidaemia. We therefore assessed the associations between the most common variant of the PPAR-gamma, the Pro12Ala (P12A) substitution in the PPAR-gamma 2 gene, with BMI, blood pressure, fasting plasma glucose, HbA1c, total cholesterol, LDL and HDL cholesterol and plasma triglyceride in 183 treatment-naïve patients with type 2 diabetes (T2D). The P12A allele associated with lower fasting plasma glucose but had no influence on HbA1c or BMI. In obese patients (BMI > 29 kg/m2), the P12A substitution associated with elevated total and non-HDL cholesterol levels.