Mitochondria play a central role in cellular energy metabolism and signaling, and their dysfunction is associated with a wide range of diseases. Therefore, assessing mitochondrial function is essential for understanding their role in various cellular processes and disease progression. Here, we describe the principles and methodologies for analyzing mitochondrial membrane potential, reactive oxygen species, and calcium levels using the fluorescent probes tetramethylrhodamine methyl ester, MitoSOX, and Rhod-2AM, respectively. This work provides a practical guide for researchers investigating mitochondrial function under physiological and pathological conditions. (c) 2025 The Author(s). Published by Elsevier Inc. on behalf of Korean Society for Molecular and Cellular Biology. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).