The novel eCell system maintains the activity of the entire repertoire of metabolic Escherichia coli enzymes in cell-free protein synthesis. We show that this can be harnessed to produce proteins with selectively 13 C-labelled amino acids from inexpensive 13 C-labelled precursors. The system is demonstrated with selective 13 C labelling of methyl groups in the proteins ubiquitin and peptidyl-prolyl cis-trans isomerase B. Starting from 3- 13 C-pyruvate, 13 C-HSQC cross-peaks are obtained devoid of one-bond 13 C- 13 C scalar couplings. Starting from 2- 13 C-methyl-acetolactate, single methyl groups of valine and leucine are labelled. Labelling efficiencies are 70 % or higher, and the method allows us to produce perdeuterated proteins with protonated methyl groups in a residue-selective manner. The system uses the isotope-labelled precursors sparingly and is readily scalable.