Abstract The aim of this study is to evaluate the expression of cytokines in response to mineral trioxide aggregate (MTA) plus selenium in germ-free mice with experimental furcal perforation. The first left maxillary molar was opened, and the furcal area was perforated and treated with post-MTA-Se (experimental group). The same surgical intervention was performed for the maxillary right first molar, which was treated with MTA (control group). Fifteen mice were sacrificed 7, 14, and 21 days after furcal perforation, and periapical tissue samples were collected. The mRNA expression levels of the cytokines TGF-β, TNF-α, IFN-γ, HPRT, IL-10, IL-4, RANK, RANKL, IL-1, and IL-17 were assessed by using real-time polymerase chain reaction. In the experimental group, at 21-days post-MTA-Se sealing, the mRNA levels of TNF-α and IL-10 were upregulated compared with those in the control group (p < 0.05). Futher assessment revealed basal mRNA expression levels of IL-1α, IFN-γ, RANK, RANKL, IL-17A, IL-4, and TGF-β, over long experimental times, in both the experimental and control groups (p > 0.05). In conclusion, MTA+Se sealing favoured increased expression of IL-10 and TNF-α at later time points (day 21).