Abstract Background Vaginal epithelial cells (VECs) produce antimicrobial peptides including human β-defensin 2 (hBD2) and secretory leukocyte protease inhibitor (SLPI), as well as cytokines and chemokines that play vital roles in mucosal innate immunity of the female reproductive tract. Houttuynia cordata Thunb ( H. cordata ), a herbal plant found in Asia, possesses various activities including antimicrobial activity and anti-inflammation. As inflammation and infection are commonly found in female reproductive tract, we aimed to investigate the effects of H. cordata water extract in modulating innate immune factors produced by VECs. Methods Primary human VECs were cultured and treated with H. cordata at a concentration ranging from 25–200 μg/ml for 6 or 18 h. After treatment, the cells and culture supernatants were harvested. The expression of hBD2 and SLPI mRNA was evaluated by quantitative real-time reverse transcription PCR. Levels of secreted hBD2 and SLPI as well as cytokines and chemokines in the supernatants were measured by ELISA and Luminex assay, respectively. Cytotoxicity of the extract on VECs was assessed by CellTiter-Blue Cell Viability Assay. Results H. cordata did not cause measurable toxicity on VECs after exposure for 18 h. The expression of hBD2 and SLPI mRNA as well as the secreted hBD2 protein were increased in response to H. cordata exposure for 18 h when compared to the untreated controls. However, treatment with the extract for 6 h had only slight effects on the mRNA expression of hBD2 and SLPI. The secretion of IL-2 and IL-6 proteins by VECs was also increased, while the secretion of CCL5 was decreased after treatment with the extract for 18 h. Treatment with H. cordata extract had some effects on the secretion of IL-4, IL-8, CCL2, and TNF-α, but not statistically significant. Conclusions H. cordata water extract modulates the expression of antimicrobial peptides and cytokines produced by VECs, which play an important role in the mucosal innate immunity in the female reproductive tract. Our findings suggest that H. cordata may have immunomodulatory effects on the vaginal mucosa. Further studies should be performed in vivo to determine if it can enhance mucosal immune defenses against microbial pathogens.