Abstract People are constantly exposed to a wide variety of chemicals. Some of these compounds, such as parabens, bisphenols and phthalates, are known to have endocrine disrupting potencies. Over the years, these endocrine disrupting chemicals (EDCs) have been a rising cause for concern. In this study, we describe setup and validation of two methods to measure EDCs in human urine, using ultra-performance liquid chromatography tandem mass spectrometry. The phenol method determines methyl-, ethyl-, propyl-, n-butyl- and benzylparaben and bisphenol A, F and S. The phthalate method determines in total 13 metabolites of dimethyl, diethyl, diisobutyl, di-n-butyl, di(2-ethylhexyl), butylbenzyl, diiso-nonyl and diisodecyl phthalate. Runtime was 7 and 8 min per sample for phenols and phthalates, respectively. The methods were validated by the National Institute of Standards & Technology (NIST) for 13 compounds. In addition, EDCs were measured in forty 24-h urine samples, of which 12 EDCs were compared with the same samples measured in an established facility (Rigshospitalet, Copenhagen, Denmark). The intra-assay coefficient of variability (CV) was highest at 10% and inter-assay CV was highest at 12%. Recoveries ranged from 86 to 115%. The limit of detection ranged from 0.06 to 0.43 ng/mL. Of 21 compounds, 10 were detected above limit of detection in ≥93% of the samples. Eight compounds were in accordance to NIST reference concentrations. Differences in intercept were found for two compounds whereas slope differed for six compounds between our method and that used in the Danish facility. In conclusion, we set up and validated two high-throughput methods with very short runtime capable of measuring 5 parabens, 3 bisphenols and 13 different metabolites of 8 phthalates. Sensitivity of the phenol method was increased by using ammonium fluoride in the mobile phase.