An adequate analytical method for determination of amino acids can provide a better insight in the metabolism of in vitro human embryo cultures, increasing the success rate of embryo implantation. Since individual amino acid amounts per embryo occur in the nanogram range, GC was the technique of choice, due to its inherent sensitivity and high sample throughput. Amino acids were analyzed as alkyl formate derivatives. The limits of detection (LOD) of all amino acids involved were in the sub-nmol range. The high risk of sample contamination proved to be the major analytical issue, but it could be overcome. For an extended method sensitivity, a simple preconcentration step could also be used.