Chkrootkit is not available for Windows but there are some alternatives that runs on Windows with similar functionality. The best Windows alternative is TDSSKiller, which is free. If that doesn't suit you, our users have ranked six alternatives to Chkrootkit and five of them are available for Windows so hopefully you can find a suitable replacement. Other interesting Windows alternatives to Chkrootkit are GMER (Free), Trend Micro RootkitBuster (Free), Sophos Virus Removal Tool (Free) and RootkitRevealer (Free).
Scan for hidden files, registry entries, processes, services, drivers, kernel code patches, ports, operating system service hooks, and Master Boot Record (MBR) rootkits. Clean or remove hidden files, registry entries, and services.
RootkitRevealer is an advanced rootkit detection utility. It runs on Windows NT 4 and higher and its output lists Registry and file system API discrepancies that may indicate the presence of a user-mode or kernel-mode rootkit.