This paper deals with a particular aspect of a wider work-in-progress centring on epidemics and economics in Mediterranean Africa. The analysis of the maritime aspects of this phenomenon is preceded by a discussion of three key and interlinked factors, i.e. the weight of epidemic outbreaks in maritime intercourse; western prejudice about the fatalist attitude of Muslim peoples in the face of epidemics; and the response of the Muslim authorities as regards health matters. It subsequently considers briefly the matter of compliance with and violation of quarantine regulations and the complaints and negotiations involving captains, consuls and local maritime authorities from the eighteenth century to the middle of the nineteenth century. It studies four complementary aspects: the decisions of governors and the extent of local administrators’ applications of these; the observation and violation of quarantine measures; lazarettos and quarantine conditions; and, finally, the rationalization of the system during the latter part of the period under consideration which paved the way for more extensive reforms under the colonial administration.