Ubiquitinated protein aggregates are observed in the brains of Alzheimer's, Parkinson's and Huntington's disease patients and in other neurodegenerative disorders. These aggregates indicate that the ubiquitin proteasome system may be impaired in these diseases. To date no therapy is available that specifically targets this system, although preventing aggregate formation or stimulating the degradation of already formed aggregates by targeting components of the ubiquitin proteasome system is an attractive therapeutic approach. Here, we review the role of the ubiquitin proteasome system in aggregate formation with respect to neurodegenerative diseases, discussing the unfolded protein response, endoplasmic reticulum-associated degradation, aggresome formation and accumulation as well as aggregation and neurotoxicity of proteins involved in neurodegeneration. The potential of pharmacological intervention within this system in patients suffering from neurodegenerative diseases will be evaluated.