The complete coding sequences of three porcine genes - NDP, CLN3 and NCF1 - were amplified using the reverse transcriptase polymerase chain reaction (RT-PCR) based on the conserved sequence information of the human, mouse, and referenced highly homologues pig ESTs. The sequence analyses of these three genes revealed that porcine NDP gene encodes a protein of 133 amino acids which has high homology with the Norrie disease protein homolog (NDP) of four species: bovine (98%) human (96%), crab-eating macaque (96%) and mouse (95%). The porcine CLN3 gene encodes a protein of 438 amino acids which has high homology with the ceroid-lipofuscinosis, neuronal 3 (CLN3) of four species: human (90%), crab-eating macaque (90%), dog (89%) and mouse (83%). The porcine NCF1 gene encodes a protein of 392 amino acids that has high homology with the neutrophil cytosolic factor 1(NCF1) of three species: bovine (87%), human (82%) and mouse (79%). Phylogenetic tree analysis revealed that the porcine NDP and NCF1 has closer genetic relationships with the bovine NDP and NCF1, but the porcine CLN3 has a closer genetic relationship with the CLN3 of human and crab-eating macaque. The tissue transcription profile analyses indicated that pig CLN3 and NCF1 genes were generally expressed in most of tissues, pig NDP gene was expressed in muscle, spleen, brain, lung but not expressed in kidney, liver, backfat and pancreas. These data serve as a foundation for further research on these three genes which have been associated with human disease.