Background: The CE mark is a mandatory European conformity marking for medical devices (MD) sold within European Economic Area. After meeting the requirements of the CE mark MD are subject to further national appraisals leading to differences in methodologies in France and Germany. HTA (Health Technology Assessment) reports aim to inform governmental players about medical, social, and economic implications of development, diffusion, and use of health technology. HTA intends to provide a bridge between the world of research and the world of decision-making. There is little information on the differences between France and Germany regarding the assessment on MD. What differences apply to the participating HTA and national bodies? Which methodology to assess innovative MD do the countries apply? This comparative health analysis clarifies the impact of HTA on reimbursement on MD and illustrates hurdles both for manufacturers and governmental players. Results: The participating HTA bodies in France are HAS and CEPS; IQWiG and g-BA in Germany. Their iterative work leads to an assessment and finally to reimbursement. Although the scope of work regarding HTA of HAS is broader, HAS and IQWiG are both independent, transparent bodies conducting appraisals on MD. CEPS and g-BA are rounding off the appraisals and make decisions (predominantly in camera). Hurdles for new MD are high in both countries regarding information needed on evidence and benefit. For very innovative MD France has introduced economical evaluations and measurements such as QALY and ICERs. In Germany on the other hand, an early benefit appraisal will be launched (2015) to address MD of risk level 2b and 3 in mainly inpatient care softening the boundaries between out- and inpatient care. Discussion: Including information such as QALYs and ICERs into decision-making is a new concept in ‘old Europe’. The impact of this new French methodology on decision-making of the CEPS is yet unclear. The role and need are questionable if they do not have a direct impact on decision-making but rather ‘inform’ as it is the case in France. By contrast, Germany aims to include broader appraisals on MD in inpatient care focusing on another field of interest: The two yet separate ‘markets’ of out- and inpatient care. Conclusion: In the last years both countries show tendencies to improve evidence-based decision-making by taking efficiency measurements and safety considerations into account. A combination of both systems regarding economic analyses and the early-benefit assessments would be preferable.