Autophagy is commonly characterized by the redistribution of the microtubule-associated light chain 3 (LC3) protein into cytoplasmic puncta, coinciding with its lipidation, as well as by a decrease in the abundance of autophagic substrates including p62 and ubiquitinylated proteins. Here, we describe a cell line, A549-B480, which, in contrast to its parental A549 line, exhibits massive accumulation of LC3 (or a GFP-LC3 fusion protein) in cytoplasmic puncta. These puncta co-localize with accumulated p62 and ubiquitinylated proteins, yet are not enwrapped by membranes. Indeed, LC3 is not lipidated in A549-B480, even when these cells are cultured in conditions in which A549 cells would develop autophagy. A549-B480 cells have been selected for their resistance against the microtubule-stabilizing agent epothilone B and actually require the continuous presence of epothilone B for their survival. Parental A549 cells treated with epothilone B manifested all signs of bona fide autophagy. In contrast, the autophagic program of A549-B480 was defective, irrespective of the absence or presence of epothilone B, and correlated with the complete absence of Atg7, a protein that is reputed to be essential for autophagy. These results establish novel functional links between microtubules and autophagy, identify a new chemotherapy resistance-associated autophagic defect, and describe the existence of LC3 puncta outside from autophagosomes.