This report is the first demonstration of the use of uncoated and dynamically coated capillaries for the separation of individual mitochondria via CE. Currently, the analysis of individual mitochondria relies upon fused-silica capillaries coated with a hydrophilic polymer (e.g. poly(acryloylaminopropanol)), which is used to minimize adsorption to the capillary surface. Both uncoated fused-silica capillaries and 0.2% w/w poly(vinyl alcohol) dynamic coating solutions are used to successfully analyze isolated individual mitochondrial particles using CE-LIF While it was possible to separate mouse liver mitochondria on an uncoated capillary, rat liver mitochondria proved to have strong adsorption characteristics that only allowed them to be adequately separated with a PVA dynamic coating or a poly(acryloylaminopropanol) (AAP) capillary. The possible causes for this adsorption are analyzed and discussed. This study shows that uncoated and dynamically coated capillaries can be used in place of AAP-coated capillaries to analyze mitochondria and suggests the use of these capillaries for the analysis of other organelles, offering a greatly simplified method for the analysis of individual organelles.