 While a student, Ussishkin took part in many digs; among those were the excavations of Chalcolithic Beersheba (late 5th millennium BC) and of the Chalcolithic burial caves in that region, under Jean Perrot; the excavations of Megiddo, under Yigael Yadin; Caltepe, in Turkey, under Tahsin Özgüç; In 1960–1961 he was Yigael Yadin's chief assistant in the excavations of the Cave of Letters, in Nahal Hever, the Judaean Desert.Documents from the period of the Bar Kokhba Rebellion were discovered in this cave, among those are some letters issued by Bar Kokhba's headquarters.During 1961 and 1962 he participated in the excavations of Ein Gedi under Benjamin Mazar.