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Margolies authored over 55 books on Jewish topics. He possessed a photographic memory, and was well versed in all aspects of both the written Bible, Oral Torah (Talmud and its commentaries) and Kabbalah (Zohar etc.). He established the Rambam library.
He wrote on a wide range of subjects; His works were meant for both scholars and laymen alike. All of his writings are in Hebrew.
He further wrote on the Kabbalah. Such works include "The Rambam and the Zohar" demonstrating correlations between Maimonides Mishneh Torah and the Zohar; Nitzotzei Zohar demonstrating correlations between the Tannatic and Amoraic works (such as the Talmud and Medrashim) and the Zohar.
He was also involved in a controversy with Gershon Scholem over the Rabbi Jacob Emden/Rabbi Jonathan Eybeshuetz controversy. Margulies produced a pamphlet defending R. Eybeshuetz and in response Scholem produced his own disagreeing with Marguleis's conclusions.
He wrote a number of scholarly biographies of major Jewish personalities such as Maharsha, Ohr Ha-Chaim Hakodosh, Noam Elimelech, Rabbi Moses ben Nachman (Ramban), and R' Yechiel of Paris including valuable annotation clarifying ideas in their works. The biographies focus primarily on their methods of scholarship and not on their personalities. First printed in Poland, they were never reprinted.
He wrote several works concerning the development of a legal system in the newly formed Jewish State (Kavei Ohr, Tal Techiyah).
According to Dr. Yitzchok Raphael, his writing is in a terse style designed to concentrate a maximum amount of information in a minimum of space.
- Toldot Adam (Lemberg 1912) on R. Shmuel Edels, also known by the acronym "Maharsha"
- Kav Bashamaim (Lemberg 1913), notes on the writings of the Tosafists
- Kavei Ohr and Tal Techiya (Lemberg 1921), two volumes on Jewish law in the Land of Israel, and essays on various topics, including "Medicine and Healers in the Talmud", "The Laws of Ger Toshav", and the first printing of "Yesod Hamishna Va'arichatah"
- Yesod Hamishna Va'arichatah (Lemberg, printed on its own first in 1923, then 1933, with addendums in Jerusalem 1956) on the creation of the Mishna
- Sefer Hasidim (Lemberg 1924, Jerusalem 1957, 1960, 1964, 1970) by Rabbi Yehuda Hachassid, with biographical information, commentaries, and his own notes titled Mekor Hessed
- Tolodot Rabbenu Hayyim ben Atar (Lemberg, 1925), biography on the Ohr ha-Hayyim includes the notes of Rabbi Meir Dan Plotzky (Kli Chemdah)
- Ohr Meir (Lemberg 1926, Tel-Aviv 1964), biography of R. Meir of Przemyślany
- Margenita d'Reb Meir (Lemberg 1926, Germany 1948, Tel-Aviv 1964), sayings of the above R. Meir
- She'elot Uteshuvot Min Hashamayim (Lemberg 1926, 1929, Jerusalem 1957), the responsa of R' Yaakov the Tosafist, who claimed to have received answers to questions of Jewish law from an angel, with R. Margolios's extensive notes, as well as a comprehensive introduction discussing prophecy and its effect on Jewish law and other related topics
- Yalkut Margoliot (Lemberg 1927), homiletic material for Sabbaths and holidays, and various times of the year
- Imrei Kadosh Hashalem (Lemberg 1928)
- Vikuach Rabbenu Yehiel miParis (Lemberg, 1928), the disputation of Rabbi Yehiel of Paris in 1240, with biography of R. Yehiel
- Mekor Hesed (Lemberg 1928)
- Lecheker Shemot Vekinuyim Batalmud (Lemberg 1928, Jerusalem 1960), on names and nicknames in the Talmud
- Hilula D'Tzidkaya (Lemberg 1929, Tel-Aviv 1930, 1961), a collection of different views and customs of great Torah scholars
- Vikuach HaRamban (Bilgoraj 1928), the disputation of Nachmanides against Pablo Christiani in 1263, with his notes
- Butzina D'Nehora Hashalem (Bilgoraj 1930)
- Gevurat Ari (Lemberg 1930)
- Toldot Rabbenu Avrohom Maimoni (Lemberg 1930), biography of the son of Maimonides, Rabbi Abraham ben HaRambam, including his responsa translated from the original Arabic
- Mekor Baruch (Lemberg 1931)
- Shem Olam (Lemberg 1931, 1962), an attempt to discover the authorities behind the Talmudic phrase "One said... and one said..." in Midrash, Babylonian Talmud, and Jerusalem Talmud
- Nefesh Haya (Lemberg 1932, Tel-Aviv 1954), notes on Shulchan Orakh Orakh Haim
- Hagadah shel Pesach (Tel-Aviv 1937, 1950), with commentary
- Sichot Chachamim (Tel-Aviv 1938), a collection of sayings and quotes from various rabbinic sages
- Ner LaMaor (Bilgoraj 1932, Jerusalem 1959), notes and emendations on the book Ohr HaHaim by Rabbi Haim ben Atar
- Mekor Habracha (Lember 1934), on clarifying the concept of making a blessing for a Torah commandment "al asiyatan", as well as the formulation of the blessings
- Zohar (Jerusalem 1940-1946, 1960) with his extensive notes (multiple printings)
- Sibat Hitnagduto (Tel-Aviv 1941), discussing the R. Emden/R. Eybeschitz controversy
- Mal'ache Elyon (Jerusalem 1945, 1964) on angels in the thought of Hazal
- Olelot (Jerusalem 1947), essays on various topics
- Tekunei Zohar (Tel-Aviv 1948), a kabbalistic work attributed to Rabbi Shimon Bar Yohai, with extensive notes by Rabbi Margolies
- Sefer HaBahir (Jerusalem 1951), a kabbalistic work attributed to Rabbi Nehunye Ben HaKaneh with extensive notes by Rabbi Margolies
- Zohar Hadash (Jerusalem 1953), a collection of statements from the Zohar, arranged according to the weekly portion. Includes a discussion of the tradition of the Zohar, as well as comparisons of sayings from the Talmud and Midrash, with the Zohar
- Milchamot Hashem (Jerusalem 1953), the famous book by Rabbi Abraham ben HaRambam about the controversy surrounding his father, Maimonides. This version is based on the manuscript from the Vatican. The introduction is a biography of Rabbi Abraham ben HaRambam by Rabbi Morgolies
- Mefarshei HaTalmud (Jerusalem 1954-1961), a commentary on some parts of the Talmud
- Shaarei Zohar (Jerusalem 1957) notes on the Talmud directing one to the relevant passages in Zohar.
- Margalios HaYam (Jerusalem 1958), a commentary on Sanhedrin
- D'varim B'Itam (Tel-Aviv 1959), homiletic material for Sabbaths and holidays and various times of the year
- HaMikra Vehamesora (Jerusalem 1964, 1965), various articles relating to issues of chain of tradition in Judaism, as well as other various topics
- Mechkarim Bedarkei Hatalmud Vechidotav (Jerusalem 1967), varied essays on the Talmud
- Peninim U'Margoliyot A posthumously published collection of essays.
There is also a memorial volume edited by Dr. Yitchak Raphael and published by Mossad R' Kook, which describes these and more books in more detail.