Proper control of mitochondrial turnover is critical for maintenance of cellular 
energetics under basal and stressed conditions, and for prevention of endogenous 
oxidative stress. Whole organelle turnover is mediated through macroautophagy, a 
process by which autophagosomes deliver mitochondria to the lysosome for 
hydrolytic degradation. While mitochondrial autophagy can occur as part of a 
nonselective upregulation of autophagy, selective degradation of damaged or 
unneeded mitochondria (mitophagy) is a rapidly growing area in development, 
cancer, and neurodegeneration, particularly with regard to Parkinson's disease. 
Due to its dynamic nature, and the potential for regulatory perturbation by 
disease processes, no single technique is sufficient to evaluate mitophagy. 
Here, we describe several complementary techniques that include electron 
microscopy, single cell analysis of LC3 fluorescent puncta, and Western blot, 
each used in conjunction with a flux inhibitor to trap newly formed 
autophagosomes in order to monitor mitophagy in neuronal cells.