Amyloid deposition, neuronal dystrophy and synaptic loss are characteristic pathological features of Alzheimer’s disease (AD). We have used cortical neuronal cultures to assess the dystrophic effect of fibrillar amyloid β (Aβ) and its relationship with neurotoxicity and synaptic loss. Treatment with fibrillar Aβ led to the development of neuritic dystrophy in the majority of the neurons present in the culture. Morphometric analysis and viability assays showed that neuronal dystrophy appeared significantly earlier and at lower Aβ concentrations than neurotoxicity, suggesting that both effects are generated independently by different cellular mechanisms. The development of dystrophic features required Aβ fibril formation and did not depend on the presence of the RHDS adhesive domain in the sequence of Aβ. Finally, a dramatic reduction in the density of synaptophysin immunoreactivity was closely associated with dystrophic changes in viable neurons. These results suggest that aberrant plastic changes and loss of synaptic integrity induced by fibrillar Aβ may play a significant role in the development of AD pathology.