I have used several different dyes to stain mitochondria, including rhodamine 123 and DiOC(6), but have found the MitoTracker dyes from Molecular Probes to be the most satisfactory for several reasons7. This family of dyes is available in different forms that may be selected for different wavelengths. They are very specific for active mitochondria, producing very little background staining. The MitoTrackers are cell permeable - cells are labeled by adding the stain to the culture medium for a period of time during which it accumulates in the organelles. This property makes it suitable for live cell microscopy, but it is also fixable using aldehydes, facilitating double-label immunofluorescence. Lastly, they are fairly photostable, unlike the other dyes I have tried. I cannot provide specific protocols for using MitoTracker dyes, as different cells accumulate the dye at variable rates and concentrations. Molecular probes provides protocols for determining optimal staining procedures in the technical information packaged with the product.