Autosomal dominant polycystic kidney disease (ADPKD) is characterized by the presence of fluid-filled cysts that grow over time. Total kidney volume (TKV) is one of the main biomarkers of disease progression, and is estimated through the technique of stereology. We tested whether patients’ kidney size impacted inter-rater reliability using the same stereology protocol. Stereology yielded excellent inter-rater reliability at both early and late stage disease, however, some pathology would still benefit from expert guidance in determining kidney tissue. This technique can easily be translated to animal models of ADPKD.