Phthalates, bisphenol A (BPA) and parabens (PBs), organic chemicals widely used in everyday products, are considered to be endocrine disruptors. We propose a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the determination of seven phthalate metabolites, six PBs and BPA in human urine. All three categories of the above endocrine disruptors were simultaneously extracted from 1 mL of human urine using solid phase extraction. In addition, with a conventional reversed phase LC column, we achieved for the first time the separation of three pairs of structural isomers, namely iso-/n-butyl paraben, propyl paraben and monobutyl phthalate. LC-MS/MS was operated and tested in both electrospray ionisation (ESI) and atmospheric pressure chemical ionisation (APCI). ESI was selected for the analysis due to its superior stability and repeatability. The method limit of detection (mLOD), achieved for a single set of high-performance LC conditions, ranged from 0.01 to 0.84 ng/mL for phthalate metabolites, from 0.06 to 0.24 ng/mL for PBs and was 2.01 ng/mL for BPA. Derivatisation of BPA with dansyl chloride lowered its mLOD to 0.007 ng/mL. Blank contamination was non-detectable. The present method was successfully applied for the analysis of the above-mentioned compounds in 80 male human urine samples.