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Introduction & Objectives: The combination of chromatographic methods with mass spectrometry is a widely applied analytical method for global metabolic profiling. Our aim was to perform LC-MS/MS study to compare levels of carnitines and amino acids in COPD patients and healthy volunteers. Methods: COPD patients for this study were recruited from Czech Multicenter Database of COPD. The analysis of blood samples was performed by triple-quadruple tandem mass spectrometer with a positive electrospray ionization probe with a designed MS/MS program for automatic profiling of acyl-carnitines and amino acids. Results: We analyzed 24 subjects with COPD, 10 controls and 6 with ischemic heart disease (IHD), out of which 4 had COPD. Small variations between the three groups were noted, most notably the C0/AC ratio where it was significantly decreased in COPD patients compared to the control p=0.001, COPD 0.59 (0.49; 0.68), IHD 0.65 (0.53; 0.74), Control 0.73 (0.57; 0.86). The analysis of amino acids shoved a lower level of Alanine in the COPD and IHD group, compared to the control. The value was statistically significantly lower in the IHD patients in comparison to control. COPD 152.50 (92.80; 226.00), IHD 107.65 (0.00; 156.00), Control 175.00 (118.00; 210.00) p=0.039. FFMI had a positive effect on Alanine blood levels in COPD patients (Sp. coef. 0.478, p=0.021).With increased age, higher levels of C14 (Sp. coef. 0.765, p= 0.010), Phelnylalnine (Sp. coef. 0.671, p= 0.034) and Phenylalanine/Tyrosine ratio (Sp. coef. 0.694, p= 0.026) were found in the control group. Conclusion: The long-term systemic effects of COPD may be marked by changes in metabolism and be reflected by altered concentrations of specific metabolites.