Our aim was to show the benefits and limitations of histological assessment of healing supported by implantable biomaterials. We reviewed and showed photographs of the histological and immunohistochemical methods applicable for the assessment of desirable and undesirable effects of biomaterials on the healing of hard and soft tissues. Currently used methods for evaluating the microscopic effects of bioengineered materials on the recipient tissue are reviewed. For histopathological analysis, semiquantitative scoring systems can be used. Alternatively, the main tissue constituents may be quantified using continuous variables giving the numerical densities of cells, lengths of microvessels or connective tissue fibres, area surfaces, area and volumes fractions, or clustering and colocalization of microscopic objects. Using systematic uniform random sampling strategies at the level of tissue blocks, sections, and image fields leads to a reasonable low variability of the quantitative results.