The relation between logic and philosophy of science, often taken for granted, is in fact problematic. Although current fashionable criticisms of the usefulness of logic are usually mistaken, there are indeed difficulties which should be taken seriously — having to do, amongst other things, with different “scientific mentalities’ in the two disciplines (section 1). Nevertheless, logic is, or should be, a vital part of the theory of science. To make this clear, the bulk of this paper is devoted to the key notion of a “scientific theory” in a logical perspective. First, various formal explications of this notion are reviewed (section 2), then their further logical theory is discussed (section 3). In the absence of grand inspiring programs like those of Klein in mathematics or Hilbert in metamathematics, this preparatory ground-work is the best one can do here. The paper ends on a philosophical note, discussing applicability and merits of the formal approach to the study of science (section 4).