The quality control (QC) system of the endoplasmic reticulum (ER) is an important monitoring mechanism in the protein maturation process, which ensures export of properly folded proteins from the ER. Incorrectly or incompletely folded proteins are retained in the ER for refolding or degradation by the ER-residing proteasome. The calnexin/calreticulin cycle and ER-associated degradation are the key elements in QC. These two mechanisms work together to allow incorrectly folded proteins have additional opportunities to achieve their native conformations. The QC dysfunction is involved in many diseases caused by mutant proteins, many of which are causes of neurodegenerative disorders. A better understanding of molecular regulation in the QC system will uncover the molecular pathogenic mechanisms of many diseases caused by protein misfolding and help discover novel strategies for preventing or treating these diseases.