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Unlike other high-income countries, Canada has no national policy for drugs treating rare diseases (orphan drugs). Nevertheless, in 2022, the Canadian government committed to creating a national strategy to make access to these drugs more consistent. Our aim was to study whether recommendations made by the Canadian Agency for Drugs and Technology in Health (CADTH) translated into coverage decisions for orphan drugs in Ontario, the largest Canadian province. This study is the first to look at this question for orphan drugs, which are at the center of policy attention. We included 155 orphan drug-indication pairs approved and marketed in Canada between October 2002 and April 2022. Cohen's kappa was used to test the agreement across health technology assessment (HTA) recommendations and coverage decisions in Ontario. Logistic regression was used to test which factors, relevant to decision-makers, might be associated with funding in Ontario. We found only fair agreement between CADTH's recommendations and coverage decisions in Ontario. Although a positive and statistically significant association between favorable HTA recommendations and coverage was found, more than half of the drugs with a negative HTA recommendation were available in Ontario, predominately through specialized funds. Successful pan-Canadian pricing negotiations were a strong predictor of coverage in Ontario. Despite efforts to harmonize access to drugs across Canada, considerable room for improvement remains. Introducing a national strategy for orphan drugs could help increase transparency, consistency, promote collaborations, and make access to orphan drugs a national priority. • Recommendations by the Canadian Agency for Drugs and Technology in Health do not always translate to provincial coverage decisions for new drugs. • We explored whether Canadian Agency for Drugs and Technology in Health's recommendations are aligned with coverage decisions for orphan drugs in Ontario. • Negative health technology assessment recommendations did not necessarily translate to no pan-Canadian pricing negotiations. • More than half the drugs with negative health technology assessment recommendations were available in Ontario through specialized funds. • A national strategy for orphan drugs could prioritize access to these treatments at a national level and harmonize access, at least to some extent, across Canada. [ABSTRACT FROM AUTHOR]