BACKGROUND Hospital mergers began in the UK in the late 1990s to deal with underperformance. Despite their prevalence, there is a lack of research on how such organizational changes affect the staff morale. This study aims to assess the impact of NHS hospital mergers between financial years 2009/10 and 2011/12 on staff job satisfaction and to identify factors contributing to satisfaction. METHODS Data on staff job satisfaction were obtained from the annual NHS Staff Survey. A list of mergers was compiled using data provided by the Cooperation and Competition Panel and the Department of Health. Other sources of data included the NHS Hospital Estates and Facilities Statistics, the NHS 'Quarter' publication, official reports from health service regulators, individual hospitals' annual accounts, data from the NHS Information Centre and the NHS Recurrent Revenue Allocations Exposition Book. Only full mergers of acute and mental health hospitals were analyzed. Propensity scores were generated using observable factors likely to affect merger decision to select three comparable hospitals for every constituent hospital in a merger to act as a control group. A difference-in-difference was estimated between baseline (3 years before merger approval) and each subsequent year up to 4 years post-merger, controlling for work environment, drivers of job satisfaction, data year, type of hospital and occupation group. RESULTS There were nine mergers during the study period. Only job satisfaction scores 1 to 2 years before (0.03 to 0.04 point) and 1 year after merger approval (0.06 point) were higher (P < 0.01) than baseline. Robustness testing produced consistent findings. Assuming other conditions were equal, an increase in autonomy, staff support, perceived quality and job clarity ratings would increase job satisfaction scores. Higher job satisfaction scores were also associated with being classified as medical, dental, management or administrative staff and working in a mental health trust. CONCLUSIONS Hospital mergers have a small, transient positive impact on staff job satisfaction in the year immediately before and after merger approval. Continuous staff support and management of staff expectations throughout a merger may help to increase staff job satisfaction during the challenging period of merger.