As they leave the Endoplasmic Reticulum (ER), properly folded and assembled proteins are selectively packaged into vesicles. These vesicles are transported by microtubule-based motor proteins and fuse together to form vesicular tubular clusters, subsequently arriving at the Golgi apparatus, a eukaryotic endomembrane organelle that often has a distinctive ribbon-like appearance.

The Golgi apparatus is a major sorting and dispatch station for the products of the ER. Newly arriving vesicles enter the cis face of the Golgi—the side facing the ER—and are transported through a collection of pancake-shaped, membrane-enclosed cisternae. Each cisterna contains unique compositions of enzymes and performs specific protein modifications. As proteins progress through the cis Golgi network, some are phosphorylated and undergo removal of certain carbohydrate modifications that were added in the ER. Proteins then move through the medial cisterna, where they may be glycosylated to form glycoproteins. After modification in the trans cisterna, proteins are given tags that define their cellular destination.

Depending on the molecular tags, proteins are packaged into vesicles and trafficked to particular cellular locations, including the lysosome and plasma membrane. Specific markers on the membranes of these vesicles allow them to dock at the appropriate cellular location. In addition, membrane phospholipids can be modified in the Golgi and the Golgi can manufacture and secrete some polysaccharides.

Interestingly, the Golgi fully disassembles and reassembles during cell division. Previously, the Golgi apparatus was understood as a static structure through which proteins progressively moved. More recently, scientists have begun to view the collection of Golgi cisternae as dynamic structures, advancing from the cis to the trans face of the network as a unit.