The mitochondria are the energy producing organelles within each cell. Decreased mitochondrial energy has been implicated in chronic fatigue, fibromyalgia and mitochondrial disease. Coenzyme Q10 is also important for its role in ATP production in the mitochondrial respiratory chain. Again, as mentioned above, methylation pathway function is necessary for the synthesis of CoQ10 in the body.

Carnitine is another nutrient produced by the body that is involved in mitochondrial energy production. Mitochondria fatty acid oxidation is the main energy source for heart and skeletal muscle. Carnitine is also involved in the transport of these fatty acids into the mitochondrial matrix. As with CoQ10, the synthesis of carnitine by the body requires methylation pathway function. Synthesis of carnitine begins with the methylation of the amino acid L-lysine by SAM, so once again we have a connection to the methionine/homocysteine pathways. Another connection between carnitine and the methylation cycle is that an enzyme that is needed for carnitine synthesis is also utilized as part of a secondary route to form methionine from homocysteine. When there are methylation cycle mutations that impair the primary route of synthesis for methionine, this secondary route will be used more heavily.