The Bakers cyst is an outpouching at the back of your knee. It is a marker that something is irritating your knee, and causing excess synovial fluid from building in the knee.
The Bakers Cyst is actually not a major problem in itself. It can cause some discomfort at the back of the knee, but it is rarely treated as it usually resolves on its own once the internal derangement of your knee is fixed.
During an arthroscopy, a Bakers cyst is not seen as it lies outside the knee joint itself. Sometimes it gets even bigger after an arthroscopy.
When a Bakers Cyst becomes troublesome, we occasionally remove them, but this requires a very careful approach, as there are a lot of major blood vessels and nerves in the same area, and if they are damaged, would lead to a poor outcome with respect to vessel damage or nerve damage. That is why there is a reluctance to perform this operation.
Our research suggests that Bakers Cysts are not that troublesome from a functional perspective. We generally just leave them to resolve on their own. Occasionally an aspiration performed in the rooms can be done to reduce the size, but if there is still irritation in the knee, it will come back.
I hope this answers your questions.
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