Coenzyme Q10 (CoQ10) and L-carnitine are very important biologically active compounds involved in energy metabolism. L-carnitine and coenzyme Q10 disturbances in mitochondrial diseases require the correction. Patients and methods: The levels of coenzyme Q10 and L-carnitine (total carnitine, free carnitine, and acylcarnitines) were determined in children with mitochondrial diseases (25 children and 16 children, respectively). High-performance liquid chromatography with UV detection (chromatograph Shimadzu Nexera LC-30) and chromatography-mass spectrometry (Agilent 6410 QQQ , USA) were used. As an additional parameter of possible coenzyme Q10 and carnitine insufficiency, the coenzyme Q10/cholesterol ratio and acylcarnitines/free carnitine ratio were calculated. Results: A significantly low ratio of coenzyme Q10/cholesterol in children with mitochondrial diseases was revealed-0.10 ± 0.01 vs. 0.19 ± 0.01 in the control group (p < 0.001). A lower absolute level of coenzyme Q10 and tendency toward a more pronounced decrease in the Q10/cholesterol ratio in older patients (6-16 years) were shown. The free carnitine blood level was within the normal range and averaged at 29.8 ± 2.6 μmol/l; however, the level was lower than that in the control group (44 ± 5.2 μmol/l, p < 0.05). A pronounced significant increase in the acylcarnitines/free carnitine ratio was determined-1.5 ± 0.05 (the normal range < 0.6).