In this paper, we critically evaulated analytical design of health technology assessment methodologies, particularly related to sensitivity analyses and willingness-to-pay thresholds. To this end, we have used two studies: the first one analyzing cost-effectiveness of a human papillomavirus vaccination of boys at age 12 against oropharyngeal carcinoma and anogenital warts and the second one examining cost-effectiveness of a universal programme of vaccinating children against pneumococcal disease. We have shown – as expected – that the impact of variation of parameters can be substantial, however, outcomes of sensitivity analyses are often understated both by marketing authorization holders and authorities. Few would disagree that innovation in health care is worthwhile; the tremendous technological success in pharmacological treatment of HIV patients is a case in point. On the other hand, a relatively large number of “me-too” entries in the pharmaceutical market and the diminishing productivity of R&D sector call for robust methodologies, which could distinguish high-value, breakthrough products. Sensitivity analyses of cost-effectiveness studies should be made pivotal in decision-making process in order to ensure efficient diffusion of innovation.