The application of Bayesian statistical analyses has been facilitated in recent years by methodological advances and an increasing complexity necessitated within research. Substantial debate has historically accompanied this analytic approach relative to the frequentist method, which is the predominant statistical ideology employed in clinical studies. While the essence of the debate between the two branches of statistics centres on differences in the use of prior information and the definition of probability, the ramifications involve the breadth of research design, analysis and interpretation. The purpose of this paper is to discuss the application of frequentist and Bayesian statistics in the pharmacoeconomic assessment of healthcare technology. A description of both paradigms is offered in the context of potential advantages and disadvantages, and applications within pharmacoeconomics are briefly addressed. Additional considerations are presented to stimulate further development and to direct appropriate applications of each method such that the integrity and robustness of scientific inference be strengthened.