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The introduction of functionalized magnetizable particles and high-gradient magnetic separation represents a time and money saving alternative to conventional purification and separation unit operations in the biotechnical sector. This technique has some advantages especially for the recycling of immobilized enzymes. A new magnetic filter with sight glasses was constructed and produced to study the performance of high-gradient magnetic separation at varied parameters. By optical analysis the buildup of a clogging was identified as the major parameter which affected the separation performance. For the cleaning procedure, a two-phase flow of water with highly dispersed air bubbles was tested which led to a nearly complete cleaning of the filter chamber.