IntroductionHealthcare-associated or nosocomial infection (HAI) is distressing to patients and costly for the National Health Service (NHS). With increasing pressure to demonstrate cost-effectiveness of interventions to control HAI and notwithstanding the risk from antimicrobial-resistant infections, there is a need to understand the incidence rates of HAI and costs incurred by the health system and for patients themselves.Methods and analysisThe Evaluation of Cost of Nosocomial Infection study (ECONI) is an observational incidence survey with record linkage and a nested case-control study that will include postdischarge longitudinal follow-up and qualitative interviews. ECONI will be conducted in one large teaching hospital and one district general hospital in NHS Scotland. The case mix of these hospitals reflects the majority of overnight admissions within Scotland. An incidence survey will record all HAI cases using standard case definitions. Subsequent linkage to routine data sets will provide information on an admission cohort which will be grouped into HAI and non-HAI cases. The case-control study will recruit eligible patients who develop HAI and twice that number without HAI as controls. Patients will be asked to complete five questionnaires: the first during their stay, and four others during the year following discharge from their recruitment admission (1, 3, 6 and 12 months). Multiple data collection methods will include clinical case note review; patient-reported outcome; linkage to electronic health records and qualitative interviews. Outcomes collected encompass infection types; morbidity and mortality; length of stay; quality of life; healthcare utilisation; repeat admissions and postdischarge prescribing.Ethics and disseminationThe study has received a favourable ethical opinion from the Scotland A Research Ethics Committee (reference 16/SS/0199). All publications arising from this study will be published in open-access peer-reviewed journal. Lay-person summaries will be published on the ECONI website.Trial registration numberNCT03253640; Pre-results.