The origin of the beth midrash, or house of study, can be traced to the early rabbinic period, following the Siege of Jerusalem (70 CE) in which the destruction of the Temple took place.
These men traced their ideological roots back to the rabbis of the late Second Temple period, specifically the Houses of Hillel and Shammai, two schools of thought.
In Lithuanian yeshivas the beth midrash will have shtenders (standing desks resembling lecterns; the Yiddish word is derived from the German Ständer).
A characteristic beth midrash has many hundreds of books, including at least several copies of the entire Talmud, Torah, Tanach, siddurim (prayer books), Shulchan Aruch, Mishneh Torah, Arba'ah Turim, Mishnah Berurah, Aruch HaShulchan and other frequently consulted works.
Also, Lee I. Levine's The Rabbinic Class of Roman Palestine in Late Antiquity, as well as the relevant articles in Dan Urman and Paul V. M. Flesher's edited volume, Ancient Synagogues: Historical Analysis and Archaeological Discovery.