Nativ was established in 1952 under the direct instruction of Prime Minister David Ben-Gurion,as a continuation of the Mossad for Aliyah Bet, an underground body , that operated within Hagana in the pre-state period, in order to allow illegal immigration of Jews despite the British Mandate authorities' restrictions.

Nativ's goals were: to maintain contact with Jews behind the Iron Curtain (then known as the "Eastern Bloc" - Eastern European countries that were under the direct and indirect control of the Soviet Union), to lift their spirits, to cultivate their connection to the State of Israel and the Jewish people and to assist their aliya to Israel. Nativ was also in charge of the world public opinion mobilization to free Soviet Jewry. Thus, exerting international pressure on the bloc countries, pressuring them to stop pursuing antisemitic policies and impose restrictions on the Jews, as well as allow their free exit to Israel. In the case of the Romanian Jews, Nativ was responsible for maintaining a direct secret contacts with Romanian communist authorities providing them material compensation for every Jew who was allowed to leave.

Due to the historical circumstances, since its establishment, Nativ has operated as part of the Israeli intelligence community and closley cooperated with its various subdivisions: the Mossad (until 1955 was also part of it), the Shin Bet and the Armed Forces and was directly subordinate to the Prime Minister. Since the fall of the Iron Curtain and the disintegration of the USSR in 1991, Nativ operates openly in accordance with the bilateral cultural-educational agreements with the FSU countries.

Nativ has been responsible for the arrival in Israel of more than two million Jews from the Soviet Union and Eastern European countries, with over 1.2 million of them immigrating to Israel from the USSR since 1989. Today Nativ is an independent unit in the Prime Minister's Office. In the early 1990s, Nativ has established Israeli Cultural Centers that operate under the patronage of the Israeli diplomatic missions. At present, nine centers are operating in the following cities: Moscow, Saint-Petersburg, Novosibirsk, Kiev, Kharkov, Odessa, Dnepr, Kishinev and Minsk. The Israeli Cultural Centers serve as a bridge to Israeli culture and language and are open to general public. Moreover, Nativ has the exclusive professional authority to examine the eligibility for Aliyah of people born in the FSU countries and in Eastern and Central Europe pursuant to the Law of Return, and is qualified to issue Aliyah visas to them.

Nativ was a full partner in the establishment of the the Israel Intelligence Heritage and Commemoration Center (IICC) and the memorial site for the fallen of the intelligence community and takes an active part in its activities.