The need to harmonize different outcome metrics is a common problem in research synthesis and economic evaluation of health interventions and technology. The purpose of this paper is to describe the use of multidimensional item response theory (IRT) to equate different scales which purport to measure the same construct at the item level. We provide an overview of multidimensional item response theory in general and the bi-factor model which is particularly relevant for applications in this area. We show how both the underlying true scores of two or more scales that are intended to measure the same latent variable can be equated and how the item responses from one scale can be used to predict the item responses for a scale that was not administered but are necessary for the purpose of economic evaluations. As an example, we show that a multidimensional IRT model predicts well both the EQ-5D descriptive system and the EQ-5D preference index from SF-12 data which cannot be directly used to perform an economic evaluation. Results based on multidimensional IRT performed well compared to traditional regression methods in this area. A general framework for harmonization of research instruments based on multidimensional IRT is described.