In the development of new medicines, assessment of a New Chemical Entities (NCEs) effect on cell number can be important for making critical decisions with regard to hazard identification or risk assessment as these effects can represent an adverse or undesirable change. Design-based stereology is the only method with the sensitivity needed to detect these small changes from histological sections with guaranteed accuracy and known precision. Practical solutions for incorporation of stereological estimates of total number in regulatory toxicology studies should provide appropriate sections for both the estimation of cell or particle number and routine histopathology evaluation in standard paraffin format from the same animal. Development of novel sampling principles, stereological software and advancements in computer hardware technology make it possible to fulfill both these criteria. The focus of this thesis work was to implement and validate three fractionators sampling procedures (Simple Fractionator, Vertical Fractionator with subsampling and Fast Fractionator) in three model organs (mouse lung, monkey urinary bladder, monkey liver). These procedures allow for enumeration of estimates of total number of alveoli, transitional epithelial cells (TECs) and hepatocytes respectively. Mean estimates of total alveolar number in mouse lungs were 6.96 X 106 (forced air) and 4.62 X 106 (smoke exposed). Mean estimates of total TECs were 63.7 X 106 (males) and 74.7 X 106 (females). Mean estimate of total hepatocyte number in male monkeys was 5.80 X 109. Design-based stereological methods can be used to estimate total cell or particle number in organs that range in both size and complexity from standard non-clinical toxicology species using novel physical fractionator designs in combination with new stereological tools and software.