Multiple System Atrophy (MSA) is an aggressive neurodegenerative disorder characterized by the formation of Glial Cytoplasmic Inclusions (GCI) containing alpha-synuclein (aSyn) fibrils in brain tissue. The fundamental causes for many neurodegenerative diseases are poorly understood, necessitating innovative approaches to study underlying mechanisms in disease development. Identifying the relevance of aSyn fibril contribution to the formation of tissue pathology, disease onset, and progression remains a central point of research interest. GCIs contain a high concentration of fibrillar material making them a well-suited target to understand the involvement of fibrils in disease development. Additionally, the high abundance of GCIs paired with the aggressiveness of MSA underscores a potential link between fibrils and disease severity and the rapid progression. This thesis aims to further understand the relevance of aSyn fibrils by using electron microscopy (EM). Using cryogenic EM allowed for the identification of multiple high-resolution structural conformers for aSyn to adapt. Improved protocols for tissue preservation permitted to characterize the brain tissue morphology by correlative light and electron microscopy (CLEM). Combining both techniques allows for linking fibril structure information to pathology formation, fibril transmission, and thus, disease progression. Key findings include 1) the identification of novel pathological inclusions and their composition in post-mortem human brain, 2) the reconstruction of the conformation of aSyn fibrils amplified from human brain homogenates, 3) successful verification of fibril transmission in a mouse model combined with 4) identification of the fibril structure and core elements potentially important in MSA severity. Furthermore, modern technology allowed to achieve the highest resolution structure to date for any aSyn fibril and to establish a working pipeline for in situ structure determination with cryogenic CLEM.