Surprisingly, glutamine synthetase was recently shown to be dual targeted to chloroplasts and mitochondria in Arabidopsis leaves. It is likely that mitochondrial glutamine synthetase assimilates ammonia, which is generated in large amounts in mitochondria during photorespiration. However, ammonia assimilation is a two-step process and the second step, catalyzed by glutamate synthase, is exclusively located in plastids. Hence, a shuttle for ammonia, possibly in the form of amino acids, is required between mitochondria and plastids. We discuss two alternative shuttles, an ornithine-citrulline shuttle and a glutamine-glutamate shuttle. Both shuttles allow the safe transport of the toxic metabolite ammonium in the form of amino acids. The ornithine-citrulline shuttle also provides a means for the transport of carbon dioxide from mitochondria to plastids, but this shuttle requires more energy than the alternative glutamate-glutamine shuttle.