With the implementation of bone substitute materials, regeneration strategies have inevitably evolved over the years. Histomorphometry is the optimal means of quantitative evaluation of bone structure and morphology. This systematic review focuses on determining study models, staining methods and histomorphometric parameters used for bone regeneration research on non-decalcified plastic-embedded specimens over the last 10 years. After being subjected to the inclusion and exclusion criteria, 118 studies were included in this review. The results establish the most commonly selected animal model is rat, followed by rabbit, sheep and dog. Strong preference for staining samples with toluidine blue was noted. With regard to histomorphometric parameters, terms related to bone were most frequently assessed, amounting to almost half of recorded parameters. New bone formation was the main descriptor of this category. Residual bone graft and non-bone tissue parameters were also often evaluated. With regard to dynamic histomorphometry, mineral apposition rate (MAR) was the parameter of choice for most researchers, with calcein green being the preferred dye for fluorochrome labelling. An overview of the contemporary literature, as well as weaknesses in the current research protocols have been discussed.