The establishment of Qasr al-Ayni medical school in Egypt under the rule of Mehmet Ali, and the supervision of Antoine Barthelemy Clot (d. 1868) ca. 1827 has been always seen as the first moment of introducing new Western medical paradigms, which were subsequently consolidated in Egypt, then Lebanon and the entire region. In dominant historiography, this ‘encounter’ was conditioned by narratives of efficacy (whereby the new medical system and technologies proved their effectiveness against a backdrop of older medical practices), and by debates of authenticity (seen to govern the relation between novel Western and traditional ‘Islamic’ practices, in the eyes of local elites). However, this dominant analysis takes for granted the claims of therapeutic efficacy as transhistorical and cross-paradigmatic, and neglects the understudied medical scene in eighteenth century Middle East including its intellectual landscape. This paper proposes that this 'encounter' should be understood within the context of medical history in the Middle East, and through analyzing the intellectual and practical priorities and positions surrounding and shaping old and emerging medical professional subjectivities. In this view, the medical paradigm that Qasr al-Ayni represented was part of a complex medical landscape that existed in the Middle East from the eighteenth through the nineteenth century, that was connected to important debates in European medicine, where Clot’s professional and intellectual positions were hardly uncontested. Through analyzing newly uncovered materials relating to medical education and practice in the Middle East from the eighteenth century on, the paper will investigate how the local medical practice, traditions of prophetic medicine, and the traditional pharmacopia interacted with European medical paradigms. It argues that Qasr al-Ayni represented a moment of colonial medical encounter in so far as it provided a tool for new medical governmentalities that relied on the school to penetrate an existing and evolving medico-scape, and to regulate the professional and paradigmatic spheres. Here, narratives of modernization, efficacy or authenticity need to be located within local sources, and local health/disease systems, which predated, surrounded and merged with the new medical systems and practitioners. To navigate this landscape, the paper will focus on two main areas, where the new medical institution interacted with existing paradigms; the pharmacopia and therapeutic technologies including disease-ecologies, and medical institutions including hospitals and their evolving roles during this period, professionalization and the development of new professional subjectivities.