Apert's medical research primarily dealt with genetic diseases and congenital abnormalities. In 1906 he documented several cases of individuals who had congenital malformations of the skull. This disorder was to become known as Apert syndrome and consists of a triad of disorders, namely craniosynostosis, syndactyly and maxillary underdevelopment.
Apert published many articles in the field of pediatrics, including an influential manual on child rearing. He was also a founding member of the French Society of Eugenics.