Changes in the tissue architecture and composition which accompany growth and development have traditionally been mapped using histological methods. The modern technology now offers new possibilities which can be used in connection with light microscopy and electron microscopy. These techniques, particularly immunohistochemistry and in situ hybridization allow studies on spatial and temporal changes in molecular patterns of substances during tissue organization and cell differentiation. In this paper, we describe the principles of immunohistology, autoradiography, and in situ hybridization, and review our recent studies in which we have applied such methods to assess craniofacial development. We have used autoradiography to localize cell proliferation and epidermal growth factor (EGF) receptors in the developing mandibular condyle. We have also used immunohistochemistry to localize the extracellular matrix component, tenascin, in differentiating chondrocytes of the mandibular condyle, employing specific antibodies. In studies on the odontogenic potential of dental papilla mesenchyme, we have used hybridoma technology, and produced monoclonal antibodies against dental papilla mesenchyme. Most recently, we have used in situ hybridization, which allows detection of gene expression in tissue sections to localize transcripts of a fibroblast-growth-factor related gene (Int-2 proto-oncogene) in developing teeth. In future, successful combination of such new histological methods and traditional experimental procedures can be expected to produce new answers to the questions about the regulation of craniofacial growth.