This study aimed to investigate the effectiveness of leaf ethanolic extract of Etlingera hemisphaerica (LE3H) in reducing defects in fetal anatomy and endochondral ossification in mice induced by HgCl2 during the post-implantation period. Pregnant mice were divided into four groups, each consisting of 10 dams, and received drink and food ad libitum. The first group was administered LE3H (E1), the second one HgCl2 (E2), the third one HgCl2+LE3H (E3), and the fourth was control (E0), administered double-distilled water only. HgCl2 (5 mg/kg bw) was administrated by injection intraperitoneally on gestation day (GD)9 and LE3H (0.39 mg/g bw) was administered by gavage on GD10. The treated and control animals were killed by cervical dislocation on GD18, dissected, and the morphologically normal living fetuses (MNLF) were collected. The MNLF of E0, E1, E2, and E3 from 5 dams were fixed with Bouin solution, and observed using the free hand razor blade technique for soft tissue examination. The remaining MNLF were fixed with 96% ethanol, and then stained with Alizarin Red S and Alcian Blue for ossification examination. Index of length of ossified part (ILOP) of humerus, index of width of ossified part (IWOP) of humerus, ILOP of femur, and IWOP of femur were calculated. E2 had higher cases of anatomical defects (74,6%) than E3 (48.9%), E1 (15.0%), and E0 (0%). E2 had humerus IWOP of 0.82±0.03, which was significantly lower than that of E0 (0.89±0.04) and E1 (0.89±0.03), while that of E1 and E0 was not significantly different from each other. Meanwhile, IWOP in E3 (0.88±0.03) was significantly higher than that in E2, but not different from that in E1 and E0. Thus, LE3H mitigated defects in fetal anatomy and endochondral ossification induced by HgCl2 in mice.