For the first time, the anatomy and histology of the epiphysis and paraphysis primordia of the gecko from the family Diplodactylidae at stage 31 are described. The epiphysis primordium of Correlophus ciliatus embryo forms median evagination of the parietal part of the roof of diencephalon. It has a tube-like structure that is oriented dorso-rostrally. The primordium has a lumen connected to the diencephalon only by a narrow canal. The transverse histological section shows that the epiphysis primordium consists of a pseudostratifaied columnar ciliated epithelium. Rare mitoses are visible in its apical part (luminal compartment). The paraphysis primordium forms median evagination of the most rostral part of the diencephalon roof. It has a tube-like structure that is oriented dorso-caudally. The primordium has a lumen connected to the brain vesicle cavity. The single-layered epithelium of the paraphysis primordium is composed of cuboidal cells. The head of the embryo is covered with single layer epithelium and periderm, the skull is absent, and the brain vesicles are surrounded by mesenchyme. Blood capillaries are attached to some local sites of the epiphysis and paraphysis primordia.