Figures from the respected Netcraft Survey in October showed that around 300,000 Web sites have stopped using Microsoft's flagship Web server in the past month.
Netcraft collated data from 33 million Web sites in what it claims to be the world's largest Web survey.
The survey found that 11% of all queried servers running IIS had the "root.exe" hacking program installed on them - up from the 8.5% found in September. This software can allow attackers to take complete control of a system.
Comments last month from analyst firm Gartner - suggesting that businesses hit by Code Red and Nimda should investigate alternatives to IIS - combined with virus threats, seem to have cut Microsoft's market share.
The biggest switch has seen around 130,000 sites moving to Microsoft's open source rival, Apache.
However, within the development community, Microsoft .Net framework is continuing to gather momentum as more developers have adopted the Microsoft Web platform. The company gained 600,000 development sites coming online.
Netcraft's survey is sent monthly as an automated query to servers to discover information such as what software runs the server, what the average server uptime is and what security flaws are present in servers.