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This work describes a method for surface regeneration of microfluidic microarray printheads through plasma techniques. Modification procedures were chosen in a way to obtain high reproducibility with a minimum of time consumption. The idea behind this is a complete regeneration of a microarray printhead before or after usage to achieve best printing results over a typical print job. A sequence of low-pressure oxygen-plasma and plasma polymerization with hexamethyldisiloxane (HMDSO) was used to regenerate printheads. Proof of the concept is given through quality control performed with a spotter implemented CCD camera, contact angle measurements and a typical hybridization experiment. Stable printing results were obtained over 3000 activations showing that the presented method is suitable for treatment of microarray printheads.