Background: Stem cells from human exfoliated deciduous teeth (SHEDs) are considered one of the most convenient sources of adult stem cells. This study aimed to examine the effect of fibroblast growth factor 6 (FGF-6) on SHEDs and evaluate CDK2 and MATK gene expression in SHED-derived microvesicles (MVs). SHEDs were cultured from deciduous teeth pulp. Methods: SHEDs were divided into two groups: the control group and test groups, with and without FGF-6 supplementation, respectively. After the third passage, SHED proliferation was assessed by MTT assay. MVs were purified and CDK2 and MATK gene expression was assessed by real time polymerase chain reaction. SHEDs were identified by their positivity for CD90 and CD73, and negativity for CD45 and CD34. Results: SHEDs proliferation in the test group was significantly higher than in the control group (P<0.001). mRNA from SHED-derived MVs from the test group exhibited a markedly elevated expression of CDK2 and MAKT, (P<0.002 and P<0.005, respectively) in comparison with those of the control group. FGF-6 enhanced the proliferation of SHEDs. Proliferation enhancement is favorable for the production of a large number of stem cells, which will then be beneficial for cell-based therapies. Conclusions: CDK2 and MAKT genes in SHED-derived MVs can be used as molecular biomarkers for SHED proliferation.