In the current paper the analytical conditions for the determination of ten free organic acids by GC-MS are studied with the aim to establish a method for organic acid profiling in human urine to be used as a tool for the detection of metabolic or other health disorders. Studies included the GC-MS method development, the derivatization (trimethylsilylation) reaction conditions, the stability of the standard solutions during storage in the freezer, and the stability of the formed trimethylsilyl derivatives. Best results were obtained at a derivatization temperature of 50°C, and a reaction time of 30 min. Standard solutions were stable for 22 days, derivatized samples were stable at least for 30 h when stored at -24°C. GC-MS analysis achieved sensitive determination of the organic acids under study with limits of detection ranging from 0.03 mmol/mol creatinine for glutaric acid, to 0.34 mmol/mol creatinine for glycolic acid. Within-day and day-to-day assay imprecision was found satisfactory with relative standard deviations being below 10%. The developed method was successfully applied to the quantitative analysis of free organic acids in urine samples obtained from hospitalized children. Creatinine-corrected excretion rates of all analyzed organic acids were within reference intervals.