The non-steroidal anti-inflammatory drug (NSAID) diclofenac, known to cause hyperuricemia and concomitant visceral gout in Gyps vultures is suggested to be a result of interference with renal uric acid excretion. Three species of Gyps vultures are on the verge of extinction due to nephrotoxic veterinary diclofenac having entered the food chain, notwithstanding the fact that the toxicity of different avian species to the NSAIDs like diclofenac varies. The multidrug resistance protein 4 (MRP4), an organic anion transporter in birds has unique role in unidirectional efflux of urate into proximal renal tubular lumen for excretion and maintenance of homeostasis. We characterized MRP4 channel at molecular level to predict its structural based ligand binding activity in Gallus domesticus (Indian domestic chicken) and Gyps himalayensis (Himalayan griffon vulture). MRP4 gene was amplified using reverse transcribed cDNA from renal tissue sample in overlapping fragments. The obtained amplicons were cloned, sequenced, assembled and analyzed. Multiple alignment and blast analysis revealed point variations and presence of additional stretch of 57 bp towards the 3' end which was confirmed in Real time PCR. Predicted MRP4 polypeptides revealed presence of characteristic 12 transmembrane helices (TMH) with two nucleotide binding domains (NBD). Additional 19 amino acids in transcript variant was found to be localized in NBD2 that might influence the transporter function. The homology modeling and pocket identification throws ample light on varying transport efficacy and paves the way for depicting its role of these amino acids in effect of diclofenac on urate transport in further studies.