This paper reviews existing case studies and methods for calibrating whole building energy models to measured data. This research describes a systematic, evidence-based methodology for the calibration of these models. Under this methodology, parameter values in the final calibrated model reference the source of information used to make changes to the initial model. Thus, the final model is based solely on evidence. Version control software stores a complete record of the calibration process, and the evidence on which the final model is based. Future users can review the changes made throughout the calibration process along with the supporting evidence. In addition to the evidence-based methodology, this paper also describes a new zoning process that represents the real building more closely than the typical core and four perimeter zone approach. Though the methodology is intended to apply to detailed calibration studies with high resolution measured data, the primary aspects of the methodology (evidence-based approach, version control, and zone-typing) are independent of the available measured data.