GCC doesn't seem to provide a c99 utility, but some vendors provide one based on gcc. And the GCC behavior can make POSIX conformance difficult to obtain. Here's the difference.
POSIX.1-2008 says[*]: -I directory Change the algorithm for searching for headers whose names are not absolute pathnames to look in the directory named by the directory pathname before looking in the usual places. Thus, headers whose names are enclosed in double-quotes ( "" ) shall be searched for first in the directory of the file with the #include line, then in directories named in -I options, and last in the usual places. For headers whose names are enclosed in angle brackets ( "<>" ), the header shall be searched for only in directories named in -I options and then in the usual places. Directories named in -I ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ options shall be searched in the order specified. Implementations shall support at least ten instances of this option in a single c99 command invocation. [*] http://www.opengroup.org/onlinepubs/9699919799/utilities/c99.html So, the directories specified by -I should have the precedence over the usual places. However, this is not the behavior of gcc; from the gcc 4.3.2 man page: -I dir Add the directory dir to the list of directories to be searched for header files. Directories named by -I are searched before the standard system include directories. If the directory dir is a standard system include directory, the option is ignored to ensure that the default search order for system directories and the special treatment of system headers are not defeated . If dir begins with "=", then the "=" will be replaced by the sysroot prefix; see --sysroot and -isysroot. As you can see, there is a difference for standard system include directories, for which the option is ignored. I suggest that GCC adds a new option to switch to the POSIX specifications. FYI, I've reported the bug against Debian here: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=533124 -- Summary: Option -I and POSIX conformance (c99 utility) Product: gcc Version: unknown Status: UNCONFIRMED Severity: enhancement Priority: P3 Component: c AssignedTo: unassigned at gcc dot gnu dot org ReportedBy: vincent at vinc17 dot org http://gcc.gnu.org/bugzilla/show_bug.cgi?id=40442