Scheduled to go live in April next year, the system will link up with those of the pathology, radiology, nursing, maternity and accident and emergency departments.
The system is part of an 11-year deal with IT healthcare specialist McKesson.
The company will also install applications for ordering tests, reporting results and issuing electronic prescriptions. These will be integrated with existing systems to give the trusts a full electronic patient record system.
Paul Street, IT project manager for both Bury and Rochdale Healthcare NHS trusts, said, "We are looking to provide an improved service and ensure that we can make all administrative and clinical data available to consultants."
The deal also includes electronic booking, allowing GPs to make patient appointments online.
Mike Eades, Rochdale NHS Trust's IM&T manager, said, "Giving clinicians modern systems and easy access to complete patient and medical information will improve patient care."
Rules-based clinical applications will help cut costs by preventing unnecessary repetition of tests, he said.
The applications will run on a range of new IBM hardware at Rochdale NHS Trust, including four xSeries application servers and an Intel-based xSeries database machine.
McKesson will run a managed service across both sites for 10 years from April next year. The trusts have struck service level agreements with the company covering availability, response times and system fix times.
McKesson is still involved in negotiations with NHS Shared Services for a massive £300m 10-year deal to update the health service's human resources and payroll systems. In June, a consortium headed by McKesson was named as the preferred supplier for the system, called Oracle HRMS.