To develop gene therapy that can be applied to glaucoma-filtering surgery, we studied effects of transfection of matrix metalloproteinase-3 (MMP-3) cDNA into rabbit conjunctiva by electroporation (EP) on changes of intraocular pressure (IOP) and bleb formation after glaucoma filtering surgery. pTracer-CMV2 vector containing MMP-3 cDNA was transfected into rabbit conjunctiva by EP and MMP-3 expression was studied by reverse transcription (RT)-PCR, zymography and western blot analysis. Three days after the EP transfection of MMP-3 cDNA or vector alone into rabbit conjunctiva, trabeculectomy was performed at the place of transfection in the presence or absence of 0.04% mitomycin C (MMC). Then changes in IOPs and bleb formation were compared with each other. Expression of MMP-3 was detected in conjunctiva until 30 days after transfection by EP. Trabeculectomy following MMP-3 transfection caused significantly longer survival of filtering bleb and decreased levels of IOP in comparison with controls (trabeculectomy alone or trabeculectomy following vector transfection), and these levels were almost identical to those of trabeculectomy with MMC. The present study indicates that EP is effective to transfect some genes that promote the filtering bleb formation in glaucoma surgery, such as MMP-3 gene, and this may be potentially applicable to glaucoma-filtering surgery in glaucoma patients.