Mitochondria are central to ATP synthesis, regulation of Ca2+ homeostasis generation of reactive oxygen species and programmed cell death. They have an essential role in generation of cell activation signals via released reactive species, as well as small GTPases, mitogen activated kinases located in the outer and inner membranes of mitochondria. While mutations of mitochondrial DNA leading to synthesis of malfunctional proteins are the most understood cause of cellular/organelle pathological changes, the mitochondrial dysfunction induced via oxidative damage to DNA, electron transport chain and structural proteins are also etiologically important events in development and progression in a wide array of diseases. This book reviews the newest discoveries supporting implication of mitochondria in inflammatory and apoptosis-based diseases.