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The social science literature on medical screening has documented a notable disjuncture between the promises of population-based screening programs and the complex realities of their rollout in everyday practice. We contribute to this scholarship by examining how healthcare providers confront numerous uncertainties associated with the implementation of anal cancer screening programs in Canada given the absence of standardized national evidence-based guidelines. The data was derived from in-depth interviews conducted with 13 physicians and 2 clinical researchers about anal cancer screening for gay, bisexual and other men who have sex with men living with HIV, the minority sub-population at the highest risk for HPV-associated anal cancer. Despite having unknown utility and low specificity, an initial anal Pap test was used to triage patients into anal dysplasia clinics for high-resolution anoscopy. This process led to technological scepticism toward the Pap's accuracy, diagnostic ambiguity related to the interpretation of the cytology results and increased patient anxiety regarding abnormal results. Physicians navigated a tension between wanting to avoid exposing their patients to additional uncertainties caused by screening and pre-cancer treatment and wanting to ensure that their patients did not develop anal cancer under their care. A high number of abnormal anal Pap results paradoxically reintroduced some of the capacity issues that the Pap was meant to resolve, as the existing dysplasia clinics were incapable of seeing all patients with abnormal results. We define this sequence as the epistemic-capacity paradox , a dynamic whereby seeking evidence to improve healthcare capacity simultaneously produces evidence that introduces capacity challenges and generates additional uncertainty. The epistemic-capacity paradox demonstrates the limitations of evidence-based medicine frameworks at determining best practices in the context of rarer health conditions affecting minority sub-populations, where smaller population numbers and limited institutional support pose systemic challenges to the acquisition of sufficient evidence. • Anal cancer rates are highest among men who have sex with men living with HIV. • Anal Pap tests are used to screen despite contested utility and uncertain results. • Limited evidence and resource constraints can create feedback loops of uncertainty. • Evidence-based medicine has critical limitations when addressing rarer conditions. • Implementing screening programs may be more difficult for minority sub-populations. [ABSTRACT FROM AUTHOR]