Mutations in the intermediate filament protein desmin cause a distinct class of myofibrillar myopathies that are characterized by deposition of aggregated desmin. To assess the effect of different disease-associated mutations at the molecular level, we applied confocal single-particle fluorescence spectroscopy. We studied the de novo aggregation properties of desmin in vitro and the aggregation state of desmin in homogenates of transfected cells rendering purification unnecessary. We detected divergent assembly patterns for 3 different desmin missense mutations. R350P-desmin showed a strong inhibition of assembly formation that was associated with a reduced level of tetramers and an increase in dimers in native cell extracts. E413K-desmin formed hyperstable tetramers. For R454W-desmin, there were subtle effects on assembly at the dimer and tetramer levels by single-particle spectroscopy that are not detectable by classical fluorescence microscopy. We also found that R350P-desmin efficiently interacts with the wild-type protein resulting in a dominant-negative effect on desmin assembly. Taken together, these results provide a molecular basis for a detailed functional classification of mutations in the desmin gene. The findings may also have implications for diagnostic and therapeutic strategies for primary desminopathies based on the different molecular events that disrupt physiological filament formation.