The aim of this paper is to review the experimental methods currently being used to evaluate the osseointegration of nanostructured titanium implants using animal models. The material modifications are linked to the biocompatibility of various types of oral implants, such as laser-treated, acid-etched, plasma-coated, and sand-blasted surface modifications. The types of implants are reviewed according to their implantation site (endoosseous, subperiosteal, and transosseous implants). The animal species and target bones used in experimental implantology are carefully compared in terms of the ratio of compact to spongy bone. The surgical technique in animal experiments is briefly described, and all phases of the histological evaluation of osseointegration are described in detail, including harvesting tissue samples, processing undemineralized ground sections, and qualitative and quantitative histological assessment of the bone-implant interface. The results of histological staining methods used in implantology are illustrated and compared. A standardized and reproducible technique for stereological quantification of bone-implant contact is proposed and demonstrated. In conclusion, histological evaluation of the experimental osseointegration of dental implants requires careful selection of the experimental animals, bones, and implantation sites. It is also advisable to use larger animal models and older animals with a slower growth rate rather than small or growing experimental animals. Bones with a similar ratio of compact to spongy bone, such as the human maxilla and mandible, are preferred. A number of practical recommendations for the experimental procedures, harvesting of samples, tissue processing, and quantitative histological evaluations are provided.