Background: Mitochondria are key players in many forms of cell death, and mitochondrial production of reactive oxygen species (ROS), membrane depolarization, permeability changes, and release of apoptogenic proteins are involved in these processes. Flow cytometric analysis of isolated mitochondria enables parallel analysis of mitochondrial structure and function in individual mitochondria, and small mitochondrial samples are sufficient for analysis. This article describes a well-characterized protocol for flow cytometric analysis of isolated liver mitochondria that can be used to detect mitochondrial alterations relevant to cell death. Methods: Fluorescent probes were used to selectively stain mitochondria (nonyl acridine orange), and to measure membrane potential (tetramethylrhodamine-methylester, 1,1Ј,3,3,3Ј,3Ј-hexamethylindodicarbocyanine-iodide), as well as production of ROS (2Ј,7Ј-dichlorodihydrofluorescein-diacetate). Calcium-induced mitochondrial swelling was detected as a decrease in SSC. To ensure optimal concentrations of all probes, the effect on mitochondrial respiration was evaluated. Results: This protocol can be used to determine the purity of the mitochondrial preparation, to detect calcium-induced morphological changes, small mitochondrial de-and hyperpolarizations, as well as physiological changes in ROS generation. Key terms: mitochondria; cell death; flow cytometry; reactive oxygen species; membrane potentials; mitochondrial permeability transition pore Mitochondrial dysfunction has been implicated as one of the key components in induction of cell death in a number of disease models. Numerous mechanisms have been proposed; for example, increased oxidative stress, altered calcium homeostasis, impairment of respiratory chain complexes, loss of membrane potential, and more recently, the activation of a pore in the inner mitochondrial membrane, the mitochondrial permeability transition pore (mPTP), with release of apoptogenic factors (1-5). Several or all of these changes may be activated in parallel during induction of cell death, posing an analytical challenge. However, using a combination of fluorescent markers and flow cytometry, several of these parameters can be studied simultaneously at the single organelle level. This approach has several advantages: (a) very small samples can be analyzed (5,000 -10,000 mitochondria), (b) preparations contaminated with other cellular constituents can be handled (using mitochondria-specific markers), (c) analysis of covariance of relevant parameters is possible, (d) potential identification of mitochondrial subpopulations, and (e) mitochondria can be sorted for further analysis of, e.g., protein profile. Also, the effects of pharmacologic agents or recombinant proteins of interest are more easily studied in isolated mitochondria than in intact cells. However, fluorescent probes can affect mitochondrial function, which may preclude or seriously limit their use (6), suggesting that a careful characterization of such a flow cytometric protocol has to be under...