The aim of this study was to investigate the possible effect of PPARalpha and PPARgamma2 variants on weight and eating attitudes as well as on their changes after 2.5-year follow-up. The study was carried out in 246 Czech non-diabetic obese women (age 49.0 +/- 11.9 years; BMI 38.1 +/- 7.0 kg/m(2)). The comprehensive weight management programme included lowenergy diet, increased physical activity and lifestyle modification. Anthropometric parameters (body weight and height, waist and hip circumferences) and body composition were measured. The Three-Factor Eating Questionnaire and Beck Depression Inventory were evaluated. At baseline and after the follow-up period, fasting levels of serum glucose, plasma adiponectin, ghrelin, leptin, and lipid profile were determined. The dependence of monitored parameters on the Pro12Ala in PPARgamma2 and Leu162Val in PPARalpha and stage of the treatment (baseline; 2.5- year follow-up) was evaluated using the repeated measures ANOVA model. The cohort was re-examined after 2.5 years, independent of regular checkups and adherence to lifestyle recommendation. Significant favourable changes in anthropometric indexes, lipid profile, leptin, ghrelin and adiponectin levels as well as in dietary restraint and hunger scores were revealed at 2.5-year check-up. However, no changes in the scores of disinhibition and depression were demonstrated. Despite several observed significant differences between carriers and non-carriers of the minor alleles at baseline and at the follow-up, the repeated measures ANOVA did not reveal any significant effect of the PPARalpha and PPARgamma2 polymorphisms on anthropometric, biochemical, hormonal and psycho-behavioural characteristics, neither at baseline nor at the 2.5-year follow-up.