The use of Three Dimensional Quantitative Structure–Activity Relationships, since its advent, has become increasingly helpful in understanding many aspects of biochemical interactions in drug research. This approach was utilized to explain the relationship of structure with biological activity of selective PPAR γ/δ agonists. The enormity of the PPAR γ/δ agonists discovery is reflected in the unprecedented speed at which research laboratories have sought to validate its clinical implications. 3D QSAR study through recently introduced k- Nearest Neighbor Molecular Field Analysis (k-NN MFA) with Step Wise (SW), Simulated Annealing (SA) and Genetic Algorithm (GA) as variable selection methods resulted in eleven statistically significant models for PPAR γ/δ agonists. These models gave a value of q2 as high as 0.7362 for model 1 and value of pred_r2 as high as 0.6985 for model 3.The k-NN MFA contour plots provided further understanding of the relationship between the structural features of PPAR γ/δ agonists derivatives and their activities, which should be applicable to design new, potential PPAR γ/δ agonists.