This protocol paper summarises a pilot of the Deep and Frequent Phenotyping (DFP) Study which builds on the infrastructure available within DPUK. This study aims to identify a set of markers that can be used as indicative outcome measures of dementia progression in the prodromal phase and in proof-of-concept trials. Markers trialled in the pilot project included PET imaging, CSF biochemistry, functional and structural MRI, gait assessment, measures of retinal pathology and the collection of biosamples. Samples were also obtained for the establishment of iPSCs for in vitro studies. This pilot study demonstrated the feasibility of conducting a study across 6 NIHR Biomedical Research Centres that are part of the NIHR Translational Research Collaboration for Alzheimer’s Disease and has provided valuable insight for the conduct of the main DFP study.