LC-MS/MS has established a critical role in clinical laboratories, but successfully implementing and maintaining LC-MS/MS testing can be challenging and resource intensive. One particularly essential, but time-consuming task when performing LC-MS/MS testing is troubleshooting problems as they arise. In this chapter, we provide a step-by-step guide for troubleshooting commonly encountered problems such as high back pressure, poor peak shape, low signal-to-noise ratios, and issues with overall analytical performance of a LC-MS/MS method. Through these specific scenarios and coinciding discussion, the goal of this chapter is teach the reader a systematic and logical approach for overcoming the unique challenges that will inevitably arise when utilizing LC-MS/MS for clinical laboratory testing.