The Conficker virus has hit a number of hospitals in Sheffield, after the Windows Security Update was disabled on 8,000 PCs during the Christmas period.
The Sheffield Teaching Hospitals Trust says the outbreak is under control and the process of "clearing-up" has begun.
David Whitham, informatics director at the Sheffield Teaching Hospitals Trust, told The Register: "We do not know how the virus entered the network but at around the same time as the virus became evident the automatic update process had been temporarily disabled following problems with a number of PCs in theatres".
Conficker targets a flaw in Windows Server Service. In October, Microsoft released an emergency security release to patch the flaw for Windows 2000, XP, Vista, Server 2003 and Server 2008. The patch was outside of its usual security cycle. However, it was revealed that 30 percent of the machines have not yet been patched with security update MS08-067, leaving millions of machines vulnerable.
The Ministry of Defence (MoD) has also been hit by the deadly virus. It was not revealed how many machines were affected but the MoD admitted that many systems, including those belonging to the Royal Navy and the Royal Airforce, were shutdown in a bid to contain and clean up the virus.