Characterising longitudinal changes in the subfields of the hippocampus using high-resolution MRI is important for understanding neurological disorders and diseases including Alzheimer’s. Hippocampus subfields are differentially involved in these disorders and can be used as biomarkers for disease. Here, we introduce an automatic longitudinal pipeline for measuring the subfields of the hippocampus (LASHiS). Unlike other longitudinal pipelines, LASHiS harnesses multiple MR contrasts and is therefore more sensitive to changes in these subfields. We compared LASHiS with four other established methods including Freesurfer and found that our method yields higher test-retest reliability and robust Bayesian longitudinal linear mixed effects modelling results.