His hope that one of the universities would recognize Jewish studies as an academic subject and appoint him to represent it was not fulfilled. Zunz for his part did not agree to the establishment of a separate seminary for fear of severing the "Science of Judaism" from the general intellectual life and leading to its isolation. He also had little use for the synods of German progressive rabbis which had begun to convene in 1844, as he could not see any benefit in their reforms. He carried on his scholarly work alone.

In Etwas ueber die rabbinische Literatur (1818) which was the first attempt to reflect Hebrew literature in all its branches, Zunz outlined the program and aims of the "Science of Judaism" and his own plan of work. According to Zunz, Jewish literature should not be shut up within the narrow confines of religious and halakhic tradition, as this literature also embraces the other humanities, as well as natural sciences. A knowledge of Hebrew literature in its broader sense would make possible the recognition of Jewish history as an inseparable part of the history of human culture in general - research into Hebrew literature is part of the humanities in general. In Zunz's opinion it is not the role of the "Science of Judaism" to influence the religious life of the modern Jew. In his proposed research program both Jews and non-Jews would join, the non-Jews' contribution being but a continuation of the scientific work of previous eras.

In Die gottesdienstlichen Vortraege der Juden, Hebrew literature, especially midrashic literature, is presented for the first time in its "historical evolution." Hundreds of works and thousands of references are combined into a single organic literary structure. Zunz describes the prophets' teaching, out of which developed the reading of the Torah and of the Prophets, the Targum, and the sermons. He dwells on the development of the Oral Law; the activities of the amoraim and the geonim and their writings; all aspects of aggadah; on preaching, its place in intellectual life; and the places of Jewish settlement in which preaching had been customary from ancient times up to the period of the maskilim and the religious reformers.

In his occupation with the "Science of Judaism" Zunz found an answer to the problems of transition from the traditional learning and the religious life based on it to modern Western education and the cultural life connected with it. He employed modern research methods to show the community of Israel and its literature as one of the trends in general intellectual life and as a participant in its progress. In so doing he denied several basic values of traditional Judaism, but in their place offered the modern Jew an interest in history. One can discern a definitely negative attitude to the area of the Talmud and the Kabbalah; he considered their spirit as opposed to that of the "Science of Judaism." It is worth noting that among the many subjects in Jewish literature Zunz chose the most "Jewish": the Midrashim and liturgical poetry. As a researcher he was precise and assiduous, demanding scientific perfection. He did not have disciples, but most of the researchers who followed him learned from him even if they did not accept his ideological premises, and his researches served as the foundation and the example for the "Science of Judaism." Not only was the latter not destined to sound the death knell of Hebrew literature, as Zunz had thought in his youth, but it was even to contribute to its revival.