OBJECTIVES: Nowadays growing number of new health technologies entering market together with more aggressive therapies administered by physicians lead to increase in number and cost of care of related adverse effects (AE). We were interested in the impact of costs of AE related to medicines not recommended for public funding by the Consultative Council (CC) of Polish Heath Technology Assessment Agency (AHTAPol) on the ground of safety issues on the Polish National Health Fund’s budget.  METHODS: Among decisions of CC published until the end of 2009, we distinguished those where safety issues were significant arguments for decline, and analyzed submissioned budget impact analyses (BIA) of those medicines in order to find the incremental costs of AE related to the treatment. Then, we compared those costs to the total incremental costs of public funding reported by manufacturers. RESULTS: Among 148 CC`s decisions analyzed, 70 were negative and in 22 safety issues were significant arguments against the positive recommendation (31% of all negative decisions). Out of 22 analyzed BIA`s only in two cases (10%) incremental costs of AE were explicitly stated, both medicines being used in oncology. In one case (4,5%), a reason for absence of those costs was stated. Stated incremental cost of AE of those two medicines was about 0,25 to 0,35 million USD in years 1 to 3 of public funding, which corresponds to about 2,5% of total incremental cost of those medicines and only 0,2% of total incremental costs of all 22 submissions (about 110 to 135 million USD). CONCLUSIONS: In submissions rejected by CC where one of the main concerns were safety issues, manufacturers failed to explicitly show the impact of costs of adverse effects of their drugs on Polish National Health Fund’s budget.