Comprehensive two-dimensional gas chromatography has been successfully applied to the analysis of various organic contaminants; however, few studies report its use in the analysis of endocrine disrupting compounds. These compounds are suspected to cause dysfunction of the endocrine system in humans and animals. This work describes the development of a method to analyse dibutylphthalate, benzylbutylphthalate, nonylphenol and octylphenol in water using solid-phase microextraction (SPME) and comprehensive two-dimensional gas chromatography with a flame ionisation detector. The merit parameters of the comprehensive two-dimensional gas chromatography with flame ionisation detector method were weighed against a gas chromatography/mass spectrometry-single ion monitoring method of endocrine disrupting compounds analysis. The compounds were evaluated over a concentration range of 0.2 to 6.0 µg L-1 . The use of a two-dimensional chromatography method proved to be advantageous in analysing endocrine disrupting compounds, according to the observed increase of the signal relative to the noise and peak resolution.