In the opening song, tattoos are described as being "chiselled in". This refers to the traditional Japanese art of tattooing, irezumi, where the ink was in former times inserted into the skin not with a needle but with chisel-like implements.
Ayato's alternate title "ollin" in the Nahuatl language of the native Mexica people of Mesoamerica means "movement". The word also forms part of the name of their sun god, Ollin Tonatiuh. Compare this with RahXephon, Rah (or Ra) being the Egyptian sun god.
The first episode opens to the overture of Wagner's "Die Meistersinger", which will later prove to be an important reference to the theme of Rahxephon - song factors heavily in this series, and the Rahxephon and the Dolems are master singers.
Reika's alternate title "ixtli", again from Nahuatl, means "face" or "eye" or "surface". This is a word with many shades of meaning, one of which is someone who has become the "face" or "eye" of a god, in the sense of a priest or priestess. Reika may well be the ixtli of RahXephon.
Two of the Mulian security units have codenames Yoknapatawpha and Macondo. Yoknapatawpha was the name used in the novels of American author William Faulkner for his home region of N. Mississippi. Similarly, Macondo is the name used in the novels of Colombian author Gabriel Garcia Marquez for his hometown. Both names are from fictionalised accounts of real places, just as Tokyo Jupiter is a "fictionalised account" by the Mulians of the real Tokyo.