Polyglutamine pathologies are neurodegenerative diseases that manifest both general polyglutamine toxicity and mutant protein-specific effects. Dentatorubral-pallidoluysian Atrophy (DRPLA) is one of these disorders caused by mutations in the Atrophin-1 protein. We have generated several models for DRPLA in Drosophila and analysed the mechanisms of cellular and organism toxicity. Our genetic and ultrastructural analysis of neurodegeneration suggests that autophagy may have a role in cellular degeneration when polyglutamine proteins are overexpressed in neuronal and glial cells. Clearance of autophagic organelles is blocked at the lysosomal level after correct fusion between autophagosomes and lysosomes. This leads to accumulation of autofluorescent pigments and proteinaceous residues usually degraded by the autophagy-lysosome system. Under these circumstances, further pharmacological and genetic induction of autophagy does not rescue neurodegeneration by polyglutamine Atrophins, in contrast to many other neurodegenerative conditions. Our data thus provide a crucial insight into the specific mechanism of a polyglutamine disease and reveal important differences in the role of autophagy with respect to other diseases of the same family. PolyQ-expanded proteins misfold and accumulate in large aggregates, which have been initially described as toxic, 1 and more recently as a positive prognosis factor in neuronal survival.2 The molecular and cellular mechanisms of toxicity due to polyQ proteins are not yet fully characterised and many of the principal aspects are under intense scrutiny. In particular, many reports have described autophagy as a protective cellular mechanism in neurodegeneration, 3 although its full contribution to the pathogenesis, including cell killing, is still poorly understood. The full cycle of autophagic degradation of cellular components and recycle of simpler constituents is not involved in cell killing. However, many dysfunctions at different steps of this cycle that have been reported upon expression of toxic proteins, including polyQ proteins, can lead to cell degeneration and death. 4 Over the past few years a growing number of studies have focused on identifying the interplay between polyQ effects and protein-specific misfunctions, 5-7 with the assumption that polyQ pathologies combine general polyQ toxicity with disease-specific effects due to the proteins affected. The fruitfly Drosophila melanogaster has proved to be a valuable model organism for polyQ diseases and neurodegeneration. New models have also moved on from initial basic observations, uncovering the complex interplay between polyQ effects and RNA or protein-specific misfunction. 5,7,9 We generated several Drosophila models of DRPLA ( Figure 1a and Supplementary Figure 1), a polyQ disease caused by mutations in atrophin-1.10,11 Atrophins are transcriptional cofactors conserved from Drosophila to mammals, 12-15 providing an ideal background for the dissection of polyQ effects and specific Atrophin functions through Drosophila ...