OBJECTIVES: To evaluate new medicines, Health Technology Assessment (HTA) agencies must have comparative data. With the lack of randomized trials versus all comparators, pharmaceutical companies have increasingly used indirect comparisons. The objective of the present study was to describe the impact of the methodology of the indirect comparison both on the ASMR determination and efficiency opinions given by the French National Authority for Health (HAS).  METHODS: Two retrospective studies were conducted in order to select HTA opinions mentioning indirect comparisons (using the keywords "indirect" or "network”) using internal databases of HAS. The first study was related on HTA opinions given by the Transparency Committee (TC) from July 2009 to October 2014. The second study analyzed efficiency opinions issued by the Commission of Economic Evaluation and Public Health (CEESP) from October 2013 to December 2014. For each study, we recorded: the method of indirect comparison used, the acceptability, the criticisms and the impact on decision-making. RESULTS: We identified 61 indirect comparisons from HTA opinions given by the TC. Among these, the TC considered 30 methodologically unacceptable. Network meta-analysis, the method recommended by the HAS, was used in 46% of cases. Only 6/61 indirect comparisons were valid, allowing to prioritize the treatment, and were consistent with the « improvement of the medical service provided » (ASMR) assigned. In the second study out of 14 opinions of efficiency given by the CEESP, 4 included indirect comparisons (29%) and they were all considered as acceptable.  CONCLUSIONS: For the TC, the results of indirect comparisons are considered as complementary evidence, and are not decisive elements for the ASMR opinion. Conversely, CEESP accepted more frequently results of indirect comparisons into economic evaluations. This apparent difference in considering and using indirect comparisons by these two commissions of the HAS may be explained by their different objectives.