During observations of mid-term and late-stage fetuses, we found a joint disk-like structure at the anterior component of the median atlanto-axial joint. At mid-term, the disk-like structure was thick (0.1–0.15 mm) relative to the sizes of bones surrounding the joint. However, it did not completely separate the joint cavity, and was absent in the inferior and/or central part of the cavity. This morphology was similar to the so-called fibroadipose meniscoid of the lumbar zygapophysial joint that is usually seen in adults. In mid-term fetuses, there was evidence suggesting that a mesenchymal tissue plate was separated from a roof of the joint cavity. In late-stage fetuses, the thickness (less than 0.15 mm) was usually the same as, or less than that at mid-term, and the disk-like structure was often flexed, folded and fragmented. Therefore, in contrast to the zygapophysial meniscoid as a result of aging, the present disk-like structure was most likely a temporary product during the cavitation process. It seemed to be degenerated in late-stage fetuses and possibly also in newborns. Anomalies at the craniocervical junction such as Chiari malformations might accompany this disk-like structure at the median atlanto-axial joint even in childhood.