Background: Mitochondrial rhomboid protease PARL mediates the cleavage of PINK1 in healthy mitochondria. Results: PARL mediates the cleavage of PGAM5 in damaged mitochondria. Conclusion: PARL regulates differential cleavage of PINK1 and PGAM5 depending on the health status of mitochondria. Significance: This is the first implication of stress-dependent regulation of PARL-mediated RIP.