Preliminary investigations aimed for fine tuning and selectionof the chromatographic conditions for the GC-MS analysis of TMSderivatives of urinary organic acids. We chose a general analyticalcolumn of wide applicability and not a “special” column designedspecifically for acids analysis. The environment of a typical clin-ical/bioanalytical laboratory, such as our laboratories, needs toaddress a series of different tasks on the analysis of a variety ofmatrices and target compounds. Target analytes of clinical rele-vancy include exogenous substances such as drugs, endogenousmetabolites such as organic acids, and toxins. Such diverse analyt-ical tasks are better served by utilizing a more generally applicableGC column.First, the effect of rate of oven temperature was studied aimingto enhance chromatographic resolution and detection sensitivity.Different oven temperature programs and ramp rates were testedwith a maximum oven temperature at 300◦C. All analytes wereeluted at an oven temperature of about 260◦C so this temperaturewas selected as the final temperature for the rest of the work.Next the gradient temperature program in the GC oven and thePTV injection mode were tested. To improve detection sensitivityand signal reproducibility, the utility of PTV inlet to allow for steeptemperature ramps (up to 700◦C/min) was exploited to developa temperature program in the injection port. This program wasadapted in relation to the properties (boiling point and density)of the sample solvent which infact is the mixture of the two derivatiz-ing agents BSTFA and TMDS that have boiling points at 45 and 57◦C,respectively.To find out the time required for cleaning the analytical col-umn after each injection of TMS derivatives of organic acids fromurine samples (back-flush mode), i.e., the time that allows elutionof highly boiling analytes, a long-time analysis of a spiked urinesample was carried out. The retention time of the latest elutingendogenous compound was about 8 min after the latest elutingorganic acid. Hence, a back-flush program (reverse flow) for 8 min