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Understanding the causes of congenital anomalies is of prime importance to develop management and/or prevention strategies. It is widely accepted that the occurrence of congenital malformations in fetuses and neonates is heavily correlated with maternal genetic makeup and lifestyle. However, very few epidemiologic analyses have been conducted on the embryonic developmental period because of the rarity of data available. Instigated in 1961, the Kyoto Collection of Human Embryos comprises approximately 45 000 specimens of embryos and fetuses. The collection's most unique feature is that most specimens were added to the collection along with epidemiologic information on the respective mothers. This is the first report on the digitization of data from the collection. A total of 22 262 embryonic specimens were selected on the basis of data integrity. Data related to the embryos were then classified according to the following criteria: developmental stage, sampling period, geographical area, maternal determinant, and external malformation. Results indicate that 7.8% of the embryos exhibit external anomalies and 92.2% are without anomalies. The three most common anomalies were nuchal bleb, holoprosencephaly and spina bifida. A special emphasis was placed on the potential association between maternal determinants and embryonic external anomalies, allowing for statistical analyses. The present study provides further evidence that this collection represents a unique source of information to conduct epidemiological analyses, not only to further the understanding of congenital anomalies but also to help establish preventive health guidelines for pregnant women.