In summary, we herein report a new method for the identification of chemical modifications at specific locations on an aptamer which improve its target binding affinity, using a high-precision automated selection process. This has resulted in improvement in affinity of up to 3.3-fold, creating some of the most strongly binding aptamers reported. We anticipate that this process could be a step-change for use of aptamers in therapeutic and analytical applications by making them competitive with antibodies not just in shelf-life, synthesis, and pharmacokinetics, but also in affinity, their single most defining feature.