Investigations play a crucial role in maintaining product quality and regulatory compliance. This chapter reviews key root cause analysis (RCA) tools—such as the Ishikawa Fishbone Diagram, Pareto Chart, 5 Whys, Fault Tree Analysis (FTA), Failure Mode and Effects Analysis (FMEA), Affinity Diagram, Scatter Plot, Variance Component Analysis (VCA), and Hypothesis Testing—and highlights their applications in systematic problem-solving. By leveraging these tools, investigators can efficiently identify root causes, prioritize issues, and allocate resources. The rationale for selecting appropriate RCA tools is discussed, emphasizing their relevance based on the problem’s complexity and available data. Regulatory citations from the FDA are analyzed to underline the critical need for robust investigation methodologies and the consequences of deficiencies. If RCA tools can be effectively applied, it can improve investigation outcomes.