Urine is a widely used matrix in biomonitoring studies on the assessment of human exposure to environmental chemicals such as phthalate esters and bisphenol A (BPA). In addition to the need to apply valid analytical techniques, assurance of specimen integrity during collection and storage is an important prerequisite for the presentation of accurate and precise analytical data. One of the common issues encountered in the analysis of non-persistent contaminants is whether shipping and storage temperature and time since collection have an effect on sample integrity. In this study, we investigated the stability of phthalate metabolites and BPA in spiked and unspiked urine samples stored at room temperature ($20^{circ}C$) or at $-80^{circ}C$ for up to 8 weeks. Concentrations of phthalate metabolites declined, on average, by 3% to 15%, depending on the compounds, and BPA declined by ~30% after 4 weeks of storage of spiked urine samples at $20^{circ}C$. In a test of 30 unspiked urine samples stored at $20^{circ}C$ and at $-80^{circ}C$ for 8 weeks, the concentrations of phthalate metabolites and BPA decreased by up to 15% to 44%, depending on the compound and on the samples. It was found that the small reduction in phthalate concentrations observed in urine, varied depending on the samples. In a few urine samples, concentrations of phthalate metabolites and BPA did not decline even after storage at $20^{circ}C$ for 8 weeks. We found a significant relationship between concentrations of target analytes in urine stored at $20^{circ}C$ and at $-80^{circ}C$ for 8 weeks. We estimated the half-lives of phthalate metabolites and BPA in urine stored at $20^{circ}C$. The estimated half-life of monoethyl phthalate (mEP) and mono (2-ethyl-5-carboxyphentyl) phthalate (mECPP) in urine stored at $20^{circ}C$ was over two years, of mono (2-ethyl-5-oxohexyl) phthalate (mEOHP) and monobenzyl phthalate (mBzP) was approximately one year, and of other phthalate metabolites was approximately 6 months. The estimated half-life of BPA in urine stored at $20^{circ}C$ was approximately 3 months, which is much longer than that reported for aquatic ecosystems.