Objectives Healthcare research performance is increasingly assessed through research indicators. We performed a systematic review to identify the indicators that have been used to measure healthcare research performance. We evaluated their feasibility, validity, reliability and acceptability; and finally assessed the utility of these indicators in terms of measuring performance in individuals, specialties, institutions and countries. Design A systematic review was performed by searching EMBASE, PsycINFO, Ovid MEDLINE and Cochrane Library databases between 1950 and September 2010. Setting Studies of healthcare research were appraised. Healthcare was defined as the prevention, treatment and management of illness and the preservation of mental and physical wellbeing through the services offered by the medical and allied health professions. Participants All original studies that evaluated research performance indicators in healthcare were included. Main outcome measures Healthcare research indicators, data sources, study characteristics, results and limitations for each study were studied. Results The most common research performance indicators identified in 50 studies were: number of publications (n = 38), number of citations (n = 27), Impact Factor (n = 15), research funding (n = 10), degree of co-authorship (n = 9), and h index (n = 5). There was limited investigation of feasibility, validity, reliability and acceptability, although the utility of these indicators was adequately described. Conclusion Currently, there is only limited evidence to assess the value of healthcare research performance indicators. Further studies are required to define the application of these indicators through a balanced approach for quality and innovation. The ultimate aim of utilizing healthcare research indicators is to create a culture of measuring research performance to support the translation of research into greater societal and economic impact.