The basic aim of the present research work is to deliver the diloxanide furoate (DF) at specific area using pectin microspheres. The microspheres were prepared by spray drying method and cross-linked by zinc acetate. Different concentrations of polymer (pectin 0.5-3%) and cross-linking agent (0-3% w/v in a mixture of ethanol:water) are taken to optimize the entrapment efficiency, swelling behavior, size and first 6h in-vitro release in simulated gastric fluids. Optimized formulation was characterized in the terms of in-vitro release, in-vivo drug disposition in various organs and in the blood of Sprague-Dawley albino rats and in-vivo gastrointestinal tract transit behavior using X-ray imaging method on albino rabbits. Findings suggested that microspheres containing a concentration of polymer (2% w/v) have average size of 100-500 μm, entrapment efficiency 85.82 ± 0.5 with swelling index 18.77 ± 5.21. In-vitro results and in-vivo gastric transit behavior (using X-ray imaging) have shown no release in first 3-6h that proved the colon specific delivery of DF. The results also suggested that the above approach have not only site specific delivery, but it improves the conversion of active drug by increasing the enzyme mediated hydrolytic degradation of DF due to the presence of polysaccharide polymer:water gel complex.