A Microsoft spokesman said the service went down at about 2pm GMT and the root cause of the outage is still unknown.
The outage affected all of Microsoft's .net Messenger Service users worldwide, including Windows Messenger and MSN Messenger subscribers, said Larry Grothaus, lead product manager for MSN.
.net Messenger Service is the back-end service that powers both the Windows Messenger and the MSN Messenger clients. The problems occurred somewhere in the .net Messenger Service, Grothaus said. MSN Hotmail e-mail service and other MSN services were unaffected.
Service was restored for some users five hours later, but a number of users were still unable to log on to the messaging software.
"It looks from what I've seen that [the service] is scaling back up. Some users may be having a little trouble getting on, but it just because it is just an issue of scaling the service back up and getting everybody back on the authentication servers," Grothaus said.