Paul Brown's script came in two days before filming was due to start and was found to be too ambitious and too unwieldy. Chris Carter set about rewriting it and continued doing so while filming took place.
The building used for the exterior of Excelsis Dei is the West Lawn building of the Riverview Hospital and has been used extensively in filming. Other uses include The Butterfly Effect (2004), Elf (2003), Deadpool (2016), Smallville (2001), Arrow (2012), Prison Break (2005) and Supernatural (2005).
In order to film the scene featuring the bathroom door bursting with water, special effects supervisor David Gauthier built a tank and flooded the set hallway with 3,300 gallons (12.5 cubic meters) of water.
A scene that revealed the attack victim Nurse Charters was a lesbian was deleted.
Scully says to Mulder "you have been reading too much Carlos Castaneda." Castaneda wrote a series of books that describe his training in shamanism, now accepted as fiction.