Objectives: Recent research has confirmed the presence of aluminium in human brain tissue. Quantitative analyses suggest increased brain aluminium content in a number of neurodegenerative diseases including familial Alzheimer's disease, congophilic amyloid angiopathy, epilepsy and autism. Complementary aluminium-specific fluorescence microscopy identifies the location of aluminium in human brain tissue and demonstrates significant differences in distribution between diseases. Herein we combine these approaches in investigating associations between aluminium in human brain tissue and specific disease-associated neuropathologies. Methods: We have used aluminium-specific fluorescence microscopy, Congo red staining using light and polarised light and thioflavin S fluorescence microscopy on serial sections of brain tissues to identify co-localisation of aluminium and amyloid ß and tau neuropathology. Results: A combination of light, polarised and fluorescence microscopy demonstrates an intimate relationship between aluminium and amyloid ß in familial Alzheimer's disease but not in other conditions and diseases, such as congophilic amyloid angiopathy and autism. We demonstrate preliminary evidence of amyloid ß pathology, including associations with vasculature and parenchymal tissues, in autism in tissues heavily loaded with aluminium. Conclusion: We suggest that complementary aluminium-specific fluorescence microscopy may reveal important information about the putative toxicity of aluminium in neurodegenerative and neurodevelopmental disorders.