Contemporary Muslim perceptions of Jews and Judaism are not always as negative and homogenous as when one thinks of ‘Arab-Muslim anti-Semitism’. The ambiguity and complexity of Indonesian Muslims' views of Judaism and Jews can be found in a number of publications by Muslims associated with interfaith organisations and Islamic universities. This article seeks to explore some nuanced, if ambivalent, perceptions of Judaism and Jews and examines factors that contributed to such perceptions among Indonesian Muslim intellectuals and authors of textbooks on religion. In most representations, the concepts of Judaism as religion and of Jewishness as ethnicity are often not distinguished. Moses, Torah, Israel and Muhammad's relationship with Jews in Medina and in medieval Spain are often discussed in the works of Indonesian Muslim intellectuals. The perceptions of Jews are based on their view of ‘Jews of Islam’ – be it in classical Medina, medieval Spain or contemporary Palestine, rather than recognising them as independent with their own dynamic history. However, Indonesian Muslim intellectuals' promotion of tolerance and pluralism serves as a response to the widely held perceptions of Judaism and Jews.