The Golgi apparatus is the main sorting compartment of the secretory pathway. At the cis Golgi cisterna, proteins are transported from the endoplasmic reticulum (ER) and sorted for forward transport or for recycling back to the ER. At the trans Golgi cisterna, proteins arriving from the medial Golgi cisterna or from endosomes are sorted for transport to the plasma membrane (PM) or to endosomes. In yeast, the Ypt1 and functional pair Ypt31/32 GTPases are required for transport at the cis and trans Golgi, respectively. The mammalian homologues of Ypt1 and Ypt31/32, Rab1 and Rab11, respectively, play similar roles. Therefore, these GTPases are considered the Golgi gatekeepers. Here, we summarize our current knowledge of upstream regulation and downstream effectors of the Golgi Ypt/Rab GTPases. In addition, we discuss the role of the Golgi Ypt/Rab GTPases in human health and disease.