Background: Efficient and accurate laboratory diagnosis of viral pathogens is of primary importance for clinical care in terms of health care system reforms. The methodological approach of cost-effectiveness analysis of laboratory diagnosis tests for viral infections from payer’s perspective was presented. We argue on an expository software-based technique for assessing the costs of newer laboratory tests. Methods: We applied decision tree modeling techniques to compare expected costs and effectiveness of strategies for the diagnosis of viral infections. We conducted univariate and Monte-Carlo method based multivariate sensitivity analysis. Results: Operating characteristics of diagnostic methods have been described. The analytical modeling, based on the cost-effectiveness method for the detection of human viruses were conducted. We considered three strategies: the use of only rapid tests for detection of one pathogen – adenoviruses; multiplexed PCR for 12 viruses, including adenoviruses; and combined strategy with confirmation of negative result of rapid test via use of PCR method. Univariative analysis showed that the cost savings achieved by use of PCR were 45% less per unit of effectiveness than the cost per effectiveness unit of rapid tests. Moreover multivariate probabilistic analysis, taking into account uncertainty of all operating characteristics, showed similar results for PCR method. Conclusions: Acceptability and usability of the applied cost-effectiveness methodology was outlined and provided in computer application for the analysis of diagnosis strategies of acute viral infections. Feasibility of study results implementation by managers was discussed to improve laboratory services and to support patient management and disease control in Ukraine.