Biochemical and genetic evidence point towards alpha-synuclein aggregation as having a pivotal role in the onset and progression of several neurodegenerative disorders, including Parkinson's disease, multiple system atrophy and Lewy body dementia. We review recent data on how alpha-synuclein aggregates may impact on cellular homeostatic mechanisms including cellular transport and degradation and transcriptional regulation. alpha-Synuclein aggregates can exist as several molecular species and their different features are discussed in the context of the methodologies used for their study and the many chemical and physical factors that influence their formation.