Brain atrophy, largely driven by tau deposition, is the most proximal correlate of cognitive decline in Alzheimer's disease (AD). Understanding the heterogeneity and longitudinal progression of brain atrophy during the disease course will play a key role in understanding the mechanisms of AD.The aim of this study is to propose a framework for longitudinal clustering that: 1) incorporates simultaneous clustering of longitudinal multivariate neuroimaging measures, 2) leverages information of individuals with irregularly sampled observations (different sampling times), 3) compares clusters with a control group, 4) allows the study and fixation of potential confounding effects, 5) can provide visualization of the resulting clusters for interpretation, 6) measures the uncertainty of clustering. We aimed to include amyloid-β positive AD patients and amyloid-β negative cognitively unimpaired (CU) subjects with longitudinal data, three sMRI scans over two years. Cortical thickness and subcortical volume measures from the longitudinal stream of FreeSurfer 6.0 pipeline were used as input for cluster analysis.Using the proposed methodology, we found 3 distinct longitudinal brain atrophy patterns in AD patients: a typical diffuse AD pattern (n=34, 47.2%), and 2 atypical AD patterns: Minimal atrophy (n=23 31.9%) and Hippocampal sparing (n=9, 12.5%). We also identified outlier observations (n=3, 4.2%) and observations with uncertain classification (n=3, 4.2%). The clusters of AD patients differed not only in regional distributions of atrophy at baseline, but also in atrophy progression over time, age at AD onset, cognitive deficits at baseline and cognitive decline over time.A framework for the longitudinal assessment of variability in cohorts with several neuroimaging measures was successfully developed and the results show that it can be used to understand heterogeneity in the context of AD.