The aim of this study was to assess the effect of the flavonoid naringin on the growth of the spheno-occipital synchondrosis by quantifying the levels of expression of Sox9 and PTHrP in an in vitro mouse model. Fifty 1-day-old BALB/c mice were randomly assigned to experimental or control groups, and each group equally divided into five time frames (6, 24, 48, 72 and 168 hours). The mice were sacrificed with phenobarbitone sodium, and the spheno-occipital synchondroses dissected and cultured in control or experimental medium, with the experimental medium supplemented with 0.1 µm naringin. Sections of the specimens underwent immunohistochemical staining for Sox9 and PTHrP, and the amount of expression was quantified using true-colour RGB (red-green-blue) computer-assisted image-analysing system with digital imaging. Data analysis showed there was a significant increase of expression of Sox9 at 6 and 24 hours (P < 0.001) between experimental and control groups, however, there was no significant difference between the levels of expression of PTHrP between experimental and control groups at any of the time frames. There was a very weak correlation found in this study between the expression of PTHrP and Sox9. In conclusion, naringin enhances the growth of the spheno-occipital synchondrosis through over expression of Sox9. This is a successful in vitro model to study factors regulating the growth of the spheno-occipital synchondrosis.