CHKB encodes one of two mammalian choline kinase enzymes that catalyze the first step in the synthesis of the major membrane phospholipid, phosphatidylcholine (PC). In humans, inactivation of the CHKB gene causes a recessive form of a rostral-to-caudal congenital muscular dystrophy. Using Chkb knockout mice, we reveal that at no stage of the disease is PC level significantly altered. Instead, at early stages of the disease the level of mitochondrial specific lipids acylcarnitine (AcCa) and cardiolipin (CL) increase 15-fold and 10-fold, respectively. Importantly, these changes are only observed in affected muscle and contribute to the decrease in the skeletal muscle functional output in these mice. As the disease progresses, AcCa and CL levels normalize and there is a 12-fold increase in the neutral storage lipid triacylgycerol and a 3-fold increase in its upstream lipid diacylglycerol. Our findings indicate that the major changes in lipid metabolism upon loss of function of Chkb is not a change in PC level, but instead is an initial inability to utilize fatty acids for energy resulting in shunting of fatty acids into triacyglycerol.