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MATLAB bundles its own, which is generally older than the system-provided version. In my case, MATLAB is bundling, whereas my distribution provides

You can try to replace the symlinks to in /usr/local/MATLAB/R2012a/bin/glnx86 and /usr/local/MATLAB/R2012a/sys/os/glnx86 to point to your system-installed version in /usr/lib. README.libstdc++ in /usr/local/MATLAB/R2012a/sys/os/glnx86 seems to indicate that at least that version is just included as a convenience. As long as the SOVERSION is the same and your system version is newer, you should be OK (and if MATLAB doesn't start, just put the symlinks back to the libstdc++ in your matlab installation folder.) I just changed the symlinks on my MATLAB installation to point to the distribution's libstdc++, it looks like I don't have any issues.