The expanding list of endocrine disrupting compounds (EDCs) has increased the need for the development of improved monitoring methods to evaluate exposure. Furthermore, the diverse physiochemical properties of EDCs impose inherent analytical limitations, and, thus, a new comprehensive method that can simultaneously analyze numerous EDCs in one chromatographic analysis would be a significant improvement over current EDC detection methods. Gas chromatography/mass spectrometry (GC/MS) offers promising profiling capabilities; however, many polar EDCs require derivatization for adequate detection. Here, a novel method for the comprehensive profiling of EDCs that employs a silyl derivatization strategy to expand the polarity range of compounds able to be separated and detected in a single chromatographic analysis is presented. The comprehensive method successfully separates 21 GC-ready and 12 derivatization-required EDCs in one chromatographic analysis. Thermal and microwave derivatization methods are effective for a comprehensive EDC mixture, although the microwave derivatization often proves more effective in shorter analysis time. A pilot-study of spiked surface water from Lake Apopka (Florida) demonstrates the potential of the comprehensive EDC profiling method.