Effectively protecting the WindowsTM OS is a challenging task, since most implementation details are not publicly known. Windows OS has always been the main target of malware that have exploited numerous bugs and vulnerabilities exposed by its implementations. Recent trusted boot and additional integrity checks have rendered the Windows OS less vulnerable to kernel-level rootkits. Nevertheless, guest Windows Virtual Machines are becoming an increasingly interesting attack target. In this work we introduce and analyze a novel Hypervisor-Based Introspection System (HyBIS) we developed for protecting Windows OSes from malware and rootkits. The HyBIS architecture is motivated and detailed, while targeted experimental results show its effectiveness. Comparison with related work highlights main HyBIS advantages such as: effective semantic introspection, support for 64-bit architectures and for recent Windows versions ($$\ge $$≥ win 7), and advanced malware disabling capabilities. We believe the research effort reported here will pave the way to further advances in the security of WindowsTM OSes.