A Baker's Cyst is a fluid-filled swelling at the back of the knee, usually on the inner (or medial) side.
This is because there is an anatomical weakness here.
Anatomical basis for a Baker's Cyst
Between the tendons of two particular muscles at the back of the knee - the gastrocnemius and the semimembranosus - there is a lubricated pocket called a 'bursa'. A bursa helps to reduce friction between structures like tendons where there is a lot of movement.
Most bursa are sealed like a closed envelope, but this particular bursa - the gastrocnemius/semimembranosus bursa - often has a communication with the joint space. Alternatively it may start life without this communication, but with age the thinner wall on the one aspect may break through creating this communication.
Once the fluid within the bursa becomes tense it is called a 'cyst'. Although a bursa is normally lubricated on its inner aspect by the cells that line it, the fluid inside the tense Baker's Cyst is normally fluid from within the knee joint itself, which may be under pressure for some reason such as osteoarthritis or a torn meniscus, so the doctor may focus initially on the underlying problem rather than the cyst itself.
A tense Baker's cyst may rupture and cause sudden painful swelling of the calf, mimicking a thrombosis.