Embryo sacs of the Korean salamander, Hynobius leechii, were collected from nine farmlands in Gyeongsangnam-Do, Korea, in early spring of 2002 and 2004. The variations in the number of embryos within each embryo sac and the mortality and abnormality rates among the embryos were investigated. We also analyzed the patterns of spontaneous embryonic malformations and the residual chemicals in the soil of the habitats using multiple-residue GC/MS. A total of 79,195 embryos were obtained from 1933 embryo sacs. There were regional variations in the length of individual embryo sacs and the number of embryos in each. The longest embryo sac averaged by region measured 20.67 cm ± 3.51 and was obtained from 2-Banseong in 2002. Of the embryos collected, 13.71% either died or stopped developing, and 3.54% of the hatched embryos developed abnormally; the latter were classified according to the patterns of malformation. External gill dysplasia was the most frequent malformation, and caudal dysplasia, abdominal blisters, and dysplasia of the fin were also observed frequently. Histopathological analysis showed neural tube abnormalities, acrania, curved notochords, thyroid teratoma, and various other kinds of endodermal developmental abnormalities. In the analysis of the residual pesticides in the soil, carbofuran, endosulfan-sulfate, and endosulfan-β were detected in the regions with high mortality and malformation rates. These results indicate that various agricultural chemicals and other unknown factors may cause the aforementioned forms of spontaneous malformations in the embryos of Hynobius leechii.