Intellectual conflicts of interest (COI), like financial COI, may threaten the validity and trustworthiness of clinical practice guidelines (CPGs). However, comparatively little is known about intellectual COI in CPGs. This study sought to estimate the prevalence of intellectual COI and corresponding management strategies among cardiology and pulmonology CPGs. We conducted a retrospective document review of CPGs published by cardiology or pulmonology professional societies from the United States, Canada, or Europe from 2018 to 2019 available via the Emergency Care Research Institute, Guidelines International Network, or Medscape databases. We assessed the percentage of authors with an intellectual COI, defined as i) authorship on a study reviewed by the CPG, ii) authorship of a prior editorial related to a CPG recommendation, or iii) authorship of a prior related CPG. Management strategies assessed included use of GRADE methodology, inclusion of a methodologist, and recusals due to intellectual COI. Outcomes were assessed overall and compared between cardiology and pulmonology CPGs. Among the 39 CPGs identified (14 cardiology, 25 pulmonology), there were a total of 737 authors, of whom 473 (64%) had at least one intellectual COI. Among all CPGs, a median of 67% (Interquartile Range 50%-76%) of authors had at least one intellectual COI, and COI was more prevalent among cardiology compared with pulmonology CPGs (84% vs 57%, p<0.001). There was variable use of management strategies among the CPGs, including use of GRADE methodology (64% of CPGs), inclusion of a methodologist (49%), and recusals due to intellectual COI (0%). Intellectual conflicts of interest appear to be highly prevalent and under-reported among cardiology and pulmonology CPGs, which may threaten their validity. Greater attention to and improved management of intellectual COI by CPG-producing organizations is needed.