Sarcosine, an isomer of l-alanine, has been recently proposed as a potential biomarker for prostate cancer risk and aggressiveness, while some studies debated its importance. As both sarcosine and l-alanine are present in human urine, it is a great challenge to separate and accurately quantify these isobaric (i.e., same m/z) compounds by chromatographic separation and mass spectrometric detection. In this study, we developed a novel 1,3-dipolar cycloaddition derivatization method that resolves sarcosine from l-alanine and allows accurate quantification of sarcosine in human urine by gas chromatography-mass spectrometry (GC-MS). This novel derivatization approach was specific to sarcosine only, while the common silylanization method resulted in overlapped derivates of both sarcosine and l-alanine. The derivatization conditions, including reagent amount, reaction temperature and time, were optimized. The method developed here has excellent precision (relative standard deviation < 4.7 %, n = 5), good linearity (slope = 0.2408; r (2) = 0.9996, 0.1-100 mu g mL(-1)), and a low limit of detection in human urine (0.15 ng mL(-1)). Application of this analytical method to urine samples spiked with standard sarcosine indicates that it is a robust and powerful alternative for resolving and quantifying sarcosine from l-alanine isomer in human urine by GC-MS.