Kidaro specialises in tools which allow administrators to manage virtualised systems.
Microsoft hopes that the purchase will allow for better management and performance of virtualised PCs on Windows software.
The software will be incorporated into Microsoft's Desktop Optimisation Pack for Software Assurance, a virtualisation package aimed at enterprise users.
Microsoft hopes that the addition will allow administrators to install and implement virtual machines on user systems more easily.
"Virtualisation technology has tremendous potential to help companies reduce costs and increase control over their desktops, while simultaneously delivering benefits to end users," said Kevin Brown, chief executive of Kidaro.
Although terms of the deal were not disclosed, media reports suggest that Microsoft spent roughly US$100m on the acquisition.
Microsoft buys virtualisation firm Kidaro
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