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On the one hand the therapy is directed against the underlying disease (cartilage damage, meniscus lesion or chronic inflammation), on the other hand, however, against the cyst itself. For a conservative therapy analgesic and anti-inflammatory medicaments are the options.

In most cases the Baker cyst decreases automatically after a succesful treatment of the underlying disease in the first place (for example a meniscus surgery) and does not have to be removed surgically.

If the Baker cyst is so large, that it causes persistent pains to the patient and if, for example, a restriction of mobility exists, it has to be removed surgically. Within the framework of an arthroscopy this is seldomly sucessful, but mostly via an open procedure. This way the cyst is laid open up until its connection to the joint capsule, removed on the whole and the gap in the joint capsule is closed up and agglutinated.