Here we show that CDK5RAP3 is weakly expressed in gastric adenocarcinoma (GA), that its expression negatively correlates with that of CD44 and is inhibited by extracellular-related kinase (ERK) signalling, and that CDK5RAP3 negatively regulate EMT and CSC phenotypes including reduced metastatic potential in gastric CSCs. Here, CDK5RAP3 is linked to gastric adenocarcinoma.