What causes carnitine deficiency?The primary condition is caused by an abnormal gene. A variety of health conditions can cause the secondary condition. These decrease the amount of carnitine in the body. They may do this by increasing the amount sent out in urine. Or, they may cause the body to absorb less from food. The health problems that can cause this include: Liver disease Kidney disease, especially with dialysis Digestive disease that causes poor absorption Malnutrition Mitochondrial disease Certain metabolic disorders Certain medicines, such as valproate