Triacyl-, diacyl- and monoacylglycerols (TAGs, DAGs, MAGs) along with monocarboxylic acids (MCAs) are intermediate products in many triacylglycerol oil-to-biofuel conversion pathways. Accumulation of these compounds leads to poor biofuel characteristics and may result in fuel system damage. We developed a method for simultaneous identification and quantification of a wide range of MCAs (C4-C18), MAGs, DAGs, and TAGs. The method is based on trimethylsilylation followed by high temperature GC with programmed temperature vaporizer (PTV) injection coupled to parallel FID and MS detectors (HTGC-FID/MS). To minimize the discrimination of both low and high molecular weight species typically occurring on the injector, we optimized injection conditions using a central composite design. The critical variables were the time at initial temperature (40 °C), splitless time, and the interaction between these two parameters. Among three tested electron ionization source/quadrupole analyzer temperatures, a 350/200 °C setting provided the highest response and signal-to-noise ratio for TAGs and did not have an effect on MAGs and DAGs. Similar results were obtained when quantifying target analytes in intermediate products of soybean oil cracking with FID and MS (using specific acylglycerol fragmentation ions). The instrumental FID limits of detection (LODs) were 0.07-0.27 ng for most of the target analytes. Selected ion monitoring (SIM) LODs were 0.01-0.05 ng for MCAs and 0.03-0.14 ng for acylglycerols. For the total ion current (TIC), LODs observed increased with acyl chain length and degree of unsaturation, resulting in an increase from 0.05 to 0.18 ng for MCAs (C5 to C18) and from 0.03 to 1.8 ng for acylglycerols (TAGs C8 to C22). Deviations in the repeatability of sample preparation, intra- and inter-day analyses, including sample stability over an eight-day time period, did not exceed 10% variance. These results demonstrate that the developed method is accurate and robust for the determination of acylglycerols and MCAs produced during the processing of TAGs into biofuels.