Our Lady of Sorrows Hospital
Scully calls Mulder from the hospital where she is working to let him know about Tad Tad O'Malley in episode 10x01 “My Struggle”. The agents talk to Sister Mary about the involvement of Augustus Goldman with the hospital in episode 10x02 “Founder's Mutation”.
Appears in 2 additional episodes.
Raymon County State Psychiatric Hospital (interior)
Mulder and Scully go inside the hospital to question Billy Miles and Peggy O'Neil and Mulder is able to confirm that Peggy has the bumps on her back in pilot episode.
Excelsis Dei (interior)
Appears in “Excelsis Dei”.
Source: Christina McClellan
Henrico County Jail
Mulder and Scully interview Arkie Seavers with his lawyer present in episode 11x03 “Plus One”.
Erindale Apartments (interior)
Mulder and Scully question the landlord at the apartment building about the mysterious tenants upstairs and then Mulder heads to the basement to search for Scully in episode 11x09 “Nothing Lasts Forever”.
Trashman Hideout (interior)
Scully and Mulder search the dark basement for the Trashman and confront the artist who created it in episode 10x04 “Home Again”.
Bethesda Naval Hospital
Mulder & Scully are summoned by some mysterious government agents to investigate some strange deaths in episode 1x06 “Shadows”.
Franklin Hospital (interior)
Daryl Landry is overseeing the homeless settlement when he follows a sound into an empty wing of the hospital in episode 10x04 “Home Again”.
Beatus Medical Center
Scully sits by her mother in the hospital while she is in a coma in episode 10x04 “Home Again”.