For calibration of internal dose in nuclear imaging, the dose model used for estimating internal dose in a patient is calibrated. One or more values of the dose model (e.g., a physics simulation, dose kernels, or a transport model) are set based on measured dose. The dose may be measured relative to specific tissues and/or isotopes, providing for tracer and tissue specific calibration. For example, dose from the tracer to be injected into the patient is estimated from emissions as well as measured by a dosimeter in a tissue mimicking tissue mimicking object. These doses are used to calibrate the dose model, which calibrated dose model is then used to determine internal dose for the patient.