The history of research on peptic ulcer disease (PUD) is usually perceived as consisting of three main phases: a) from the second half of the 19th century to the 1950s, during which two main hypotheses (the acidity and the bacterial hypothesis) were investigated in parallel; b) from the 1950s to the 1980s, during which the bacterial hypothesis was abandoned and the scientific research of PUD as well as the related medical practice were based on the acidity hypothesis; c) from the 1980s to nowadays, starting from Warren and Marshall’s discovery of the bacteria Helicobacter pylori as one of the main causes of PUD. In this paper we investigate why the bacterial hypothesis was abandoned in the 1950s, and whether there were good epistemic reasons for its dismissal. Of special interest for our research question is Palmer’s 1954 large-scale study, which challenged the bacterial hypothesis with serious counter-evidence, and which is by many scholars considered as the shifting point in the research of PUD. However, we show that: 1. Palmer’s study was methodologically problematic since it was conducted only with one specific method of identifying bacteria although there were other and arguably more reliable methods available at the time. This undermines its perceived status as a crucial experiment" against the bacterial hypothesis. 2. In view of this and other considerations we argue that the bacterial hypothesis was worthy of pursuit in the 1950s. We close the paper by indicating that the exact reason of the premature dismissal of this research program in the 1950s may belong to different social or epistemic factors that are to be investigated in future research."