Abstract Objectives This study investigates the influence of normal cohort (NC) size and the impact of different NCs on automated MRI-based brain atrophy estimation. Methods A pooled NC of 3945 subjects (NCpool) was retrospectively created from five publicly available cohorts. Voxel-wise gray matter volume atrophy maps were calculated for 48 Alzheimer’s disease (AD) patients (55–82 years) using veganbagel and dynamic normal templates with an increasing number of healthy subjects randomly drawn from NCpool (initially three, and finally 100 subjects). Over 100 repeats of the process, the mean over a voxel-wise standard deviation of gray matter z-scores was established and plotted against the number of subjects in the templates. The knee point of these curves was defined as the minimum number of subjects required for consistent brain atrophy estimation. Atrophy maps were calculated using each NC for AD patients and matched healthy controls (HC). Two readers rated the extent of mesiotemporal atrophy to discriminate AD/HC. Results The maximum knee point was at 15 subjects. For 21 AD/21 HC, a sufficient number of subjects were available in each NC for validation. Readers agreed on the AD diagnosis in all cases (Kappa for the extent of atrophy, 0.98). No differences in diagnoses between NCs were observed (intraclass correlation coefficient, 0.91; Cochran’s Q, p = 0.19). Conclusion At least 15 subjects should be included in age- and sex-specific normal templates for consistent brain atrophy estimation. In the study’s context, qualitative interpretation of regional atrophy allows reliable AD diagnosis with a high inter-reader agreement, irrespective of the NC used. Clinical relevance statement The influence of normal cohorts (NCs) on automated brain atrophy estimation, typically comparing individual scans to NCs, remains largely unexplored. Our study establishes the minimum number of NC-subjects needed and demonstrates minimal impact of different NCs on regional atrophy estimation. Key Points • Software-based brain atrophy estimation often relies on normal cohorts for comparisons. • At least 15 subjects must be included in an age- and sex-specific normal cohort. • Using different normal cohorts does not influence regional atrophy estimation.