Effectively utilizing incomplete multi-modality data for diagnosis of Alzheimer’s disease (AD) is still an area of active research. Several multi-view learning methods have recently been developed to deal with missing data,with each view corresponding to a specific modality or a combination of several modalities. However,existing methods usually ignore the underlying coherence among views,which may lead to suboptimal learning performance. In this paper,we propose a view-aligned hypergraph learning (VAHL) method to explicitly model the coherence among the views. Specifically,we first divide the original data into several views based on possible combinations of modalities,followed by a sparse representation based hypergraph construction process in each view. A view-aligned hypergraph classification (VAHC) model is then proposed,by using a view-aligned regularizer to model the view coherence. We further assemble the class probability scores generated from VAHC via a multi-view label fusion method to make a final classification decision. We evaluate our method on the baseline ADNI-1 database having 807 subjects and three modalities (i.e.,MRI,PET,and CSF). Our method achieves at least a 4.6% improvement in classification accuracy compared with state-of-the-art methods for AD/MCI diagnosis.