INTRODUCTION: We describe the protocol for a project that will use linkage of routinely collected NHS data to answer a question about the nature and effectiveness of liaison psychiatry services in acute hospitals in England. METHODS AND ANALYSIS: The project will use three data sources: (1) Hospital Episode Statistics (HES), a database controlled by NHS Digital that contains patient data relating to emergency department (ED), inpatient and outpatient episodes at hospitals in England; (2) ResearchOne, a research database controlled by The Phoenix Partnership (TPP) that contains patient data relating to primary care provided by organisations using the SystmOne clinical information system and (3) clinical databases controlled by mental health trusts that contain patient data relating to care provided by liaison psychiatry services. We will link patient data from these sources to construct care pathways for patients who have been admitted to a particular hospital and determine those patients who have been seen by a liaison psychiatry service during their admission.Patient care pathways will form the basis of a matched cohort design to test the effectiveness of liaison intervention. We will combine healthcare utilisation within care pathways using cost figures from national databases. We will compare the cost of each care pathway and the impact of a broad set of health-related outcomes to obtain preliminary estimates of cost-effectiveness for liaison psychiatry services. We will carry out an exploratory incremental cost-effectiveness analysis from a whole system perspective. ETHICS AND DISSEMINATION: Individual patient consent will not be feasible for this study. Favourable ethical opinion has been obtained from the NHS Research Ethics Committee (North of Scotland) (REF: 16/NS/0025) for Work Stream 2 (phase 1) of the Liaison psychiatry-measurement and evaluation of service types, referral patterns and outcomes study. The Confidentiality Advisory Group at the Health Research Authority determined that Section 251 approval under Regulation 5 of the Health Service (Control of Patient Information) Regulations 2002 was not required for the study 'on the basis that there is no disclosure of patient identifiable data without consent' (REF: 16/CAG/0037).Results of the study will be published in academic journals in health services research and mental health. Details of the study methodology will also be published in an academic journal. Discussion papers will be authored for health service commissioners.