- Objective We used a genome-wide approach to identify differentially expressed genes in patients with preterm premature rupture of membranes to improve the understanding of underlying molecular mechanisms. Study design RNA was isolated from the fetal membranes of patients with preterm labor with intact membranes and preterm premature rupture of membranes and was stratified according to the presence or absence of histologic chorioamnionitis. Microarray experiments were used to identify differentially expressed genes, and real-time quantitative reverse transcriptase-polymerase chain reaction and immunohistochemistry were used in follow-up experiments. Results Microarray experiments identified decreased expression of proteinase inhibitor 3 in the preterm premature rupture of membranes cases. Quantitative reverse transcriptase-polymerase chain reaction confirmed these results. Immunohistochemistry demonstrated decreased proteinase inhibitor 3 protein expression in preterm premature rupture of membranes. Conclusion A genome-wide approach identified deficient expression of proteinase inhibitor 3 in preterm premature rupture of membranes, which demonstrated the usefulness of functional genomics for the dissection of mechanisms of disease and identification of differentially regulated genes that were not suspected previously to play a role in parturition.