The trimeric G(i3) protein-dependent lysosomal-autophagic pathway is responsible for the degradation of a pool of N-linked glycoproteins in the human colon cancer HT-29 cell line. Here we have followed the fate of N-glycans using HT-29 cells either overexpressing the wild-type G alpha(i3) protein or transfected with different mutants of the G alpha(i3) protein. The stabilization of N-glycans was dependent upon the inhibition of autophagic sequestration by either 3-methyladenine (3-MA) or pertussis toxin (PTX). However, PTX allowed the processing of high-mannose glycans whereas 3-MA did not. The destabilization of the Golgi apparatus by brefeldin A, which interrupts the intracellular trafficking of N-linked glycoproteins along the secretory pathway, did not interfere with the macroautophagic pathway. These results suggest that the lysosomal-autophagic pathway is not dependent upon the integrity of the Golgi apparatus and points to differences between the molecular properties of two membrane flow processes (macroautophagy, exocytic pathway) controlled by the trimeric G(i3) protein.