Objectives Hataedock is a treatment that dispels toxic heat and meconium which has been accumulated to the fetus from a pregnant mother via orally administering herbal extracts to a newborn baby. This study was conducted to compare the efficacy of Hataedock, with using the extract of Coptis japonica & Glycyrrhiza uralensis, to the early administration of probiotics for immunomodulation in the intestinal mucosa. Methods NC/Nga mice were divided into three groups; Control group (no treatment), CGT group (3-week-old mice given the extract of Coptis japonica & Glycyrrhiza uralensis), and MBT group (3-week-old mice given a Bifidobacterium). After 2 weeks, the intestinal mucosa tissues of each group of mice were observed. Immunohistochemical staining for IL-4, IL-13, CD40, $Fc{\varepsilon}RI$, $p-I{\kappa}B$, EGF, and VEGF in the intestinal mucosa was performed. Results CGT group showed 65% decrease in IL-4, 67% decrease in IL-13, 58% decrease in CD40, 72% decrease in $Fc{\varepsilon}RI$, 76% decrease in $p-I{\kappa}B$, 41% increase in EGF and 100% increase in VEGF compared to the control group. MBT group also showed 50% decrease in IL-4, 63% decrease in IL-13, 33% decrease in CD40, 53% decrease in $Fc{\varepsilon}RI$, 46% decrease in $p-I{\kappa}B$, 23% increase in EGF and 151% increase in VEGF compared to the control group. Conclusions These results suggest that both Hataedock, with using the extract of Coptis japonica & Glycyrrhiza uralensis, and early administration of probiotics were effective in regulating Th2, relieving inflammation and developing intestinal mucosal tissues. Hataedock with extract of Coptis japonica & Glycyrrhiza uralensis may be more effective for immunomodulation in intestinal mucosa than probiotics.