The X Window System, and thus Cygwin/X, uses its own internal clipboard system that is distinct from the clipboard system used by Windows. Copying and pasting text between these two clipboard systems requires a clipboard integration program that watches for updates to either clipboard and copies data between them when either one is updated.
Cygwin/X has an internal clipboard integration system that is envoked via the -clipboard command-line parameter. See the Section called Command Line Parameters in Chapter 3 for more information on the -clipboard command-line parameter.
Note: Clipboard integration between the X Window System and Windows is not easy to provide. As of 2003-09-19, the Cygwin/X clipboard integration still suffers from a shortcoming that causes selected selected in X programs to be immediately unhighlighted. This issue is very well known and will take somewhere between 40 and 120 hours of programming to fix; no one has the time to fix it. Please do not report this to the mailing list as a bug.
Cygwin/X also has a legacy external clipboard integration system that consists of a stand-alone executable called xwinclip. xwinclip can be installed via Cygwin's setup.exe.