The data reported here demonstrate that, at least one of the functions supported by the endogenous LRRK2 kinase activity in a H4 glioma cell line and in primary astrocytes is involved in the non-canonical control of macroautophagy, working parallel to the mTOR/ULK1 pathway and dependent on PI3P and Beclin-1 activity. Here, BECN1 is linked to central nervous system cancer.