The phylogenetic history of Eichstaettisaurus has been tumultuous like that of Ardeosaurus, which has been a consequence of both incomplete data and its primitive form.
von Meyer did not provide a placement for Ardeosaurus when he named the genus; Richard Lydekker and Karl Alfred von Zittel placed it and Homoeosaurus in the Rhynchocephalia, Baron Franz Nopcsa placed Ardeosaurus as a close relative of the skinks, and Charles Camp placed it close to the Gekkonidae.
Based on the well-developed rims of the eye sockets and supratemporal fenestrae on the skull in the type specimen of E. schroederi, Broili concurred with Nopcsa's conclusion in 1938.
Within the Scincomorpha, he noted that the amphicoelous vertebrae of Ardeosaurus (including E. schroederi) best resembled that of the Xantusiidae (night lizards), as most other skinks have procoelous (convex on the rear surface) vertebrae.

Upon separating schroederi into the genus Broilisaurus, Hoffstetter retained it within the Xantusiidae in 1953, but he noticed that its skull curiously resembled those of geckoes.
Since xantusiids and geckoes were then placed on the two major recognized branches of lizards, Autarchoglossa and Ascalabota, Hoffstetter speculated that it was close to the ancestral stock of lizards.
Upon renaming it to Eichstaettisaurus, Kuhn established the family Eichstaettisauridae, still in the Xantusiidae.
In 1961 and then 1963, Cocude-Michel concurred with Camp that Ardeosauridae and Eichstaettisauridae were actually geckoes and not xantusiids, based on major differences in the postcranial skeleton, and placed both in the Gekkonomorpha.
Hoffstetter accepted this identification in 1966, as did Richard Estes in 1983.

However, phylogenetic analyses conducted by Victor Reynoso in 1996 (not published), Evans and Luis Javier Barbadillo in 1998 and 1999, and Evans and Daniel Chure in 1998 suggested that both Eichstaettisaurus and Ardeosaurus were much more basal (early-diverging) squamates.
Along with Bavarisaurus, Scandensia, and Hoyalacerta, the two were found to fall outside the crown group of Squamata.
This would make them stem-squamates, i.e. not descendants of the common ancestor of all living squamates.
However, in the 1999 analysis, Evans and Barbadillo acknowledged that the position of Eichstaettisaurus was unstable due to missing data (only 44% of the characteristics used in their analysis could be coded for it), and one of their phylogenetic trees placed it as the sister group to Scleroglossa among crown squamates.
Evans and colleagues found E. gouldi to be the sister group of E. schroederi in 2004, and recovered a similar position for both.

Subsequent phylogenetic analyses from Evans and colleagues found a variety of conflicting positions for Eichstaettisaurus and Ardeosaurus.
In 2005, Evans and Yuan Wang conducted two analyses, one based on a 1998 analysis by Michael Lee and the other based on Evans and Chure's 1998 analysis, but they added Dalinghosaurus, Dorsetisaurus, and Parviraptor to both.
One found Eichstaettisaurus as the sister group of a group containing Xantusiidae, Gekkonidae, Pygopodidae, and Amphisbaenia, with Ardeosaurus being close to Lacertidae and Teiioidea; the other united Eichstaettisaurus with Dalinghosaurus and the Xenosauridae in the Anguimorpha, with Ardeosaurus as the sister group of Iguania.
After Evans, Wang, and Chun Li added Yabeinosaurus to the same analyses, one found Eichstaettisaurus, Ardeosaurus, Yabeinosaurus, and Parviraptor to form the sister group to the Scleroglossa, while the other recovered Ardeosaurus as a stem-squamate and Eichstaettisaurus, Hoyalacerta, Parviraptor, and Scandensia to form a group among Scleroglossa.

A 2006 phylogenetic analysis by Jack Conrad and Mark Norell likewise found Eichstaettisaurus as close to the Scleroglossa.
In 2008, Conrad published a large phylogenetic analysis of squamates including 222 taxa and 363 characteristics, which attempted to address the problem of incomplete taxon sampling (i.e. an insufficient number of included taxa) causing phylogenetic instability.
To include Eichst
The phylogenetic history of Eichstaettisaurus has been tumultuous like that of Ardeosaurus, which has been a consequence of both incomplete data and its primitive form. von Meyer did not provide a placement for Ardeosaurus when he named the genus; Richard Lydekker and Karl Alfred von Zittel placed it and Homoeosaurus in the Rhynchocephalia, Baron Franz Nopcsa placed Ardeosaurus as a close relative of the skinks, and Charles Camp placed it close to the Gekkonidae. Based on the well-developed rims of the eye sockets and supratemporal fenestrae on the skull in the type specimen of E. schroederi, Broili concurred with Nopcsa's conclusion in 1938. Within the Scincomorpha, he noted that the amphicoelous vertebrae of Ardeosaurus (including E. schroederi) best resembled that of the Xantusiidae (night lizards), as most other skinks have procoelous (convex on the rear surface) vertebrae. 
Upon separating schroederi into the genus Broilisaurus, Hoffstetter retained it within the Xantusiidae in 1953, but he noticed that its skull curiously resembled those of geckoes. Since xantusiids and geckoes were then placed on the two major recognized branches of lizards, Autarchoglossa and Ascalabota, Hoffstetter speculated that it was close to the ancestral stock of lizards. Upon renaming it to Eichstaettisaurus, Kuhn established the family Eichstaettisauridae, still in the Xantusiidae. In 1961 and then 1963, Cocude-Michel concurred with Camp that Ardeosauridae and Eichstaettisauridae were actually geckoes and not xantusiids, based on major differences in the postcranial skeleton, and placed both in the Gekkonomorpha. Hoffstetter accepted this identification in 1966, as did Richard Estes in 1983.
However, phylogenetic analyses conducted by Victor Reynoso in 1996 (not published), Evans and Luis Javier Barbadillo in 1998 and 1999, and Evans and Daniel Chure in 1998 suggested that both Eichstaettisaurus and Ardeosaurus were much more basal (early-diverging) squamates. Along with Bavarisaurus, Scandensia, and Hoyalacerta, the two were found to fall outside the crown group of Squamata. This would make them stem-squamates, i.e. not descendants of the common ancestor of all living squamates. However, in the 1999 analysis, Evans and Barbadillo acknowledged that the position of Eichstaettisaurus was unstable due to missing data (only 44% of the characteristics used in their analysis could be coded for it), and one of their phylogenetic trees placed it as the sister group to Scleroglossa among crown squamates. Evans and colleagues found E. gouldi to be the sister group of E. schroederi in 2004, and recovered a similar position for both.
Subsequent phylogenetic analyses from Evans and colleagues found a variety of conflicting positions for Eichstaettisaurus and Ardeosaurus. In 2005, Evans and Yuan Wang conducted two analyses, one based on a 1998 analysis by Michael Lee and the other based on Evans and Chure's 1998 analysis, but they added Dalinghosaurus, Dorsetisaurus, and Parviraptor to both. One found Eichstaettisaurus as the sister group of a group containing Xantusiidae, Gekkonidae, Pygopodidae, and Amphisbaenia, with Ardeosaurus being close to Lacertidae and Teiioidea; the other united Eichstaettisaurus with Dalinghosaurus and the Xenosauridae in the Anguimorpha, with Ardeosaurus as the sister group of Iguania. After Evans, Wang, and Chun Li added Yabeinosaurus to the same analyses, one found Eichstaettisaurus, Ardeosaurus, Yabeinosaurus, and Parviraptor to form the sister group to the Scleroglossa, while the other recovered Ardeosaurus as a stem-squamate and Eichstaettisaurus, Hoyalacerta, Parviraptor, and Scandensia to form a group among Scleroglossa.
A 2006 phylogenetic analysis by Jack Conrad and Mark Norell likewise found Eichstaettisaurus as close to the Scleroglossa. In 2008, Conrad published a large phylogenetic analysis of squamates including 222 taxa and 363 characteristics, which attempted to address the problem of incomplete taxon sampling (i.e. an insufficient number of included taxa) causing phylogenetic instability. To include Eichst
Eichstaettisaurus