Internet service provider EarthLink and Webroot Software released a report that said an average of almost 28 spyware programs are running on each computer.
Trojan horse or system monitoring programs were found on more than 30% of all systems scanned, raising fears of identity theft.
The report presented the results of scans of more than one million internet-connected computers. Many of the 29 million spyware programs that were found were harmless "adware" programs which display advertising banners or track web surfing behaviours.
However, the companies also found more than 300,000 instances of programs that are capable of stealing personal information or providing unauthorised access to computers.
The Spyware programs are sometimes bundled with other software, such as peer-to-peer file sharing programs, and installed legally on users' systems. However, once installed, they run surreptitiously in the background and can be difficult to detect and remove.
The report covers the first three months of this year and information was compiled from scans conducted by both EarthLink and Webroot. It is the first of what will be regular updates that track the prevalence of spyware.
The results showed the proliferation of spyware and should encourage computer users to take steps to protect themselves.
In particular, the detection of morethan 184,000 Trojan horse programs on the systems scanned and a similar number of system monitoring programs, such as key-logging software, underscore the potential for identity theft and system compromise for internet users, said Matt Cobb, EarthLink vice-president of core applications.
The ISP began offering spyware protection for customers in October. EarthLink added a program called Spyware Blocker for free as part of its TotalAccess package of software programs and tools, which EarthLink subscribers can download from the company's website.
Paul Roberts writes for IDG News Service