Latent biomarkers are quantities that strongly relate to patient's disease diagnosis and prognosis, but are difficult to measure or even not directly observable. The objective of this study was to develop, analyze and validate new priors for Bayesian inference of such biomarkers. Theoretical analysis revealed a relationship between the estimates inferred from the model and the true values of measured quantities, and the impact of the priors. This led to a new prior encoding scheme that incorporates objectively measurable domain knowledge, i.e. by performing two measurements with a reference method, which imply scale of the prior distribution. Second, priors on parameters of systematic error are non-informative, which enables biomarker estimation from a set of different quantities. Analysis showed that the volume of nucleus basalis of Meynert, which is reduced in early stages of Alzheimer's dementia and Parkinson's disease, is inter-related and could be inferred from compartmental brain volume measurements performed on routine clinical MR scans. Another experiment showed that total lesion load, associated to future disability progression in multiple sclerosis patients, could be inferred from lesion volume measurements based on multiple automated MR scan segmentations. Besides, figures of merit derived from the estimates could, without comparing against reference gold standard segmentations, identify the best performing lesion segmentation method. The proposed new priors substantially simplify the application of Bayesian inference for latent biomarkers and thus open an avenue for clinical implementation of new biomarkers, which may ultimately advance the evidence-based medicine.