Autophagy is important in cellular homeostasis for the cell survival mechanism. 
Deficiency or excess of autophagy is generally related to some of diseases such 
as cancer and neurodegeneration. Although autophagy is a cell survival 
mechanism, it can mediate programmed cell death in several conditions. 
Autophagy-related genes (ATGs) regulate the autophagy and also control the 
crosstalk with autophagy-associated cell death and apoptosis in some condition. 
Various methods have been used to detect the marker genes and the proteins 
involved in these processes. Quantitative real-time PCR (qRT-PCR) method for 
monitoring the expression of genes involved in autophagy or autophagic cell 
death is often preferred because of its sensitivity, high efficiency potential, 
accurate quantification, and high-grade potential automation. The detection of 
the markers for autophagy-related process by immunohistochemistry in paraffin 
sections of various patient tissues has become a reliable method for monitoring 
autophagy. Here, we introduce protocols for detecting autophagy and 
autophagy-associated cell death in HeLa cells by using gene expression assays 
qRT-PCR, and also in paraffin-embedded tissue section from human biopsy material 
by using immunohistochemistry.