Rough endoplasmic reticulum (rER) consists of a network of rounded or flattened membranous sacs (cisternae) with polyribosomes covering much of the outer surface of the cisternae. Polypeptides synthesized on these ribosomes are deposited inside vesicles for eventual delivery outside of the cell or targeting to the plasma membrane or lysosomes. Proteins that are synthesized by free polysomes are destined for the cytosol, cytoskeleton, nucleus, or organelles, such as the mitochondria or peroxisomes.

Since the RNA associated with rER is basophilic, cytoplasm rich in rER shows basophilia with routine LM stains, such as H&E. This is prominent in neurons, where the basophilic patches in the cytoplasm are called Nissl or chromatophilic substance, as seen in this section of cerebellum. Basophilic rER is also prominent in secretory cells. An example of this occurs near the nucleus of cells in the pancreas.

Smooth endoplasmic reticulum.