Insulin‐dependent (type II) diabetes is characterized by an inability to metabolize glucose, resulting from insufficient insulin function for glucose transport from the blood to tissues. One cause of insufficiency is malfunction of the insulin‐producing beta cells within the pancreatic islets. Various compounds to stimulate and restore normal islet function are under development. Zucker diabetic fatty (ZDF) rat animal models are used to measure efficacy of drug candidates, as they show clinical effects similar to those in diabetic patients. Drug effects are evaluated by removing the pancreas from ZDF rats, processing the tissue with paraffin and sectioning it, and then analyzing the sections utilizing antibodies against targeted proteins to quantify morphology and metabolic activity. This protocol describes quantitative analysis of insulin, glucagon, mitochondria (all on a per‐islet basis), and insulin‐positive proliferating cells in ZDF and lean rat pancreatic tissue sections using the iCyte Imaging Cytometer. Curr. Protoc. Cytom. 56:6.32.1‐6.32.17. © 2011 by John Wiley & Sons, Inc.