The philosophy of Louis Althusser is often contrasted with the ideas of Michel Foucault. At first sight, the disagreement seems to be about the concept of ideology: while Althusser seem to be huge advocate of the use of the concept, Foucault apparently dislikes and avoids the concept altogether. However, I argue in this article that this reading is only superficial and that it obscures the real debate between these two authors. Althusser, especially in his recently posthumously published Sur la reproduction (1995), appears to agree on many points with Foucault. The real dispute lies not in the concept of ideology, but in its connection with its counterpart ‘science’. Both Althusser and Foucault were in a way epistemologists, focusing on the question on how sciences develop and how scientific practice works. Focussing on their shared background in the French epistemology, with authors such as Gaston Bachelard and Jean Cavaillès, the real discussion appears to be about whether science can really be opposed to ideology or not. Focusing on these aspects of their works can shed new lights on their oeuvre as well as on the nature of scientific practice.