Purpose: To determine the changes in the expression of transcripts of matrix metalloproteinases (MMPs) and their tissue inhibitor (TIMP) in the conjunctiva following glaucoma filtration surgery (GFS). Methods: The reverse transcription-polymerase chain reaction method was performed on tissue specimens obtained from adult rabbits undergoing GFS at various postoperative time points. Results: MMP 1 decreased more than 7-fold from its baseline level during the first 2 weeks following surgery. MMP 2 decreased on the 1st postoperative day, but increased on day 2, and remained elevated for 2 weeks. The postoperative level of MMP 14 did not change much from baseline except that noted on day 9. The TIMP 1 expression showed an early biphasic pattern. MMP 3 and MMP 9 were not detected in all the specimens. Conclusions: The transcript expression of MMPs and TIMP 1 in the conjunctiva is altered following GFS, with each gene product demonstrating a unique temporal pattern.