Reliance on evidence-based medicine requires high methodological standards from guideline developers. We sought to determine the methodological quality of guidelines on pneumonia and urinary tract infections (UTIs). We included guidelines published by national or international committees in the last 10 years providing recommendations for antibiotic type or duration. We applied the Appraisal of Guidelines for Research and Evaluation II checklist, adding under each item the specific focus relevant to bacterial infections, addressing antibiotic resistance and local epidemiology. Three assessors scored each guideline independently. Mean aggregated scores, converted to percentage per domain, are presented. We included 13 guidelines on the treatment of pneumonia and seven guidelines for the treatment of UTI. ‘Scope and purpose’ scored 69.4% for pneumonia and 71.4% for UTI. Guidelines were downgraded for lack of an epidemiological overview relevant to intended users. ‘Stakeholder involvement’ scored 39.5% for pneumonia and 44.5% UTI, with the major fault being lack of patient consultation. ‘Rigour of development’ scored 42.8% for pneumonia and 56.9% for UTI. Commonly, the search process lacked precision, no risk of bias assessment was performed, outcomes in primary studies were not critically assessed or used to direct recommendations, and there was no formal methodology for formulating recommendations. ‘Clarity of presentation’ scored highest: 67.7% for pneumonia and 68.5% for UTI. ‘Applicability’ of the guidelines in antibiotic stewardship programmes was usually not addressed: 16.9% and 25.4%, respectively. ‘Editorial independence’ scored 30.6% for pneumonia and 55.6% for UTI. Formal examination of guidelines in infectious diseases showed worrying findings related to core methodology and potential bias caused by competing interests.