Mitochondria are critical for cellular bioenergetics, and they mediate apoptosis within cells. We used whole body PPAR coactivator-1 (PGC-1) knockout animals to investigate its role on organelle function, apoptotic signalling, and cytochrome c oxidase (COX) activity, an indicator of mitochondrial content, in muscle and other tissues (brain, liver and pancreas). Lack of PGC-1 reduced mitochondrial content in all muscles (17%-44%; P<0.05) but had no effect in brain, liver and pancreas. However, the tissue expression of proteins involved in mtDNA maintenance (Tfam), import (Tim23) and remodelling (Mfn2, Drp1) did not parallel the decrease in mitochondrial content in PGC-1 KO animals. These proteins remained unchanged or were upregulated (p<0.05) in the highly oxidative heart, indicating a change in mitochondrial composition. A change in muscle organelle composition was also evident from the alterations in subsarcolemmal (SS) and intermyofibrillar (IMF) mitochondrial respiration, which was impaired in the absence of PGC-1. However, endurance trained KO animals did not exhibit reduced mitochondrial respiration. Mitochondrial reactive oxygen species (ROS) production was not affected by the lack of PGC-1, but SS mitochondria from PGC-1 KO animals released a greater amount of cytochrome c than in WT animals following exogenous ROS treatment. Our results indicate that the lack of PGC-1 results in 1) a muscle type-specific suppression of mitochondrial content which depends on basal oxidative capacity, 2) an alteration in mitochondrial composition, 3) impaired mitochondrial respiratory function which can be improved by training, and 4) a greater basal protein release from subsarcolemmal mitochondria, indicating an enhanced mitochondrial apoptotic susceptibility.