Codon Harmonizer is an online tool for the adaptation of genes to be used for heterologous protein expression. In contrast to codon optimization, the process of harmonization can be considered as a milder one. For some cases it can be advantageous that rare codons are not substituted by codons with high frequencies. Rare codons may function as regulators and give the protein time to fold through a different folding pathway to enhance correct folding and solubility. Codon harmonization can be seen as an alternative to the conventional “black box” codon optimization procedure and might help in solubilisation of the heterologously expressed proteins.