Objective This study investigated the presence and levels of matrix metalloproteinases (MMP)-2 and -9 in periapical abscesses. Study design Eighteen samples of intracanal exudates containing pus were collected from teeth with clinically and radiographically verified primary or secondary acute and chronic apical abscesses. Pro- and active forms of MMP-2 and MMP-9 levels were analyzed by using substrate gel zymography followed by an image analysis system. Statistical analysis was performed using the Kruskall-Wallis and Mann-Whitney U tests with Bonferroni adjustment. Results Both forms of MMP-9 were detected in all pus samples and demonstrated marked differences among the experimental groups ( P < .05). Primary or secondary acute apical abscess samples demonstrated significantly higher MMP-9 levels compared with MMP-2 levels ( P < .01). However, MMP-2 could not be detected in chronic apical abscesses. Conclusion According to the results of this study, gelatinases might affect the pathogenesis of acute and chronic periapical abscesses.