A multitiered strategy was adopted to assess tau conformational changes within fibrillar lesions during the progression of Alzheimer's disease (AD). Anti-tau monoclonal antibodies whose epitopes are distributed across much of the molecule were used to probe vulnerable brain regions in 37 clinically staged cases obtained from the Religious Orders Study. In this way, tau conformational changes were evaluated as the disease progressed from early cognitive decline to AD. These analyses revealed three main findings. First, the presence of granulovacuolar and fibrillar lesions correlates with several measures of episodic memory, suggesting that these lesions significantly contribute to cognitive dysfunction. Second, neuropil threads precede the appearance of neurofibrillary tangles that in turn precede the appearance of neuritic plaques. Third, tau structural changes, or "conformational signatures," emerged as a result of in situ reactivity to a subset of antibodies and nonreactivity to others, thereby reflecting the underlying status of the tau molecule within the fibrillar lesions. These signatures allowed us to document a sequence of tau conformational changes that occur during AD and to correlate these changes with episodic memory deficits. Furthermore, we were able to compare conformational signatures of tau among different lesion types and determine that the molecular profile of tau is lesion-specific.