The stereological approach can provide an objective unbiased assessment of structural change in biological systems. In this review, we elucidate the basic principles of stereology and their implementation in the analysis of tissue response to tissue-engineering scaffolds. A brief outline of tissue response parameters that can be estimated using stereological approach is included. The focus is on frequently quantified parameters in tissue response, such as host tissue infiltration, inflammatory cell numbers, angiogenesis, fibrous tissue thickness, areas of calcification, and/or necrosis, among others. Special consideration is given to sampling techniques and how these techniques can influence the reliability of the obtained results as well as minimizing potential sources of bias. These basic principles are illustrated with practical examples, where measurements are performed and estimations calculated using conventional stereological techniques. As the next generation of biomaterials continue to be developed, it is essential that researchers develop a rigorous and unbiased method of performance quantification.