Deep knee pit pain may be a symptom of a few different conditions, such as a Baker's cyst, popliteus tendinitis, or a meniscus tear. A Baker's cyst is a swelling caused by a buildup of fluid at the back of the knee. This swelling can cause pain, especially when the knee is bent or straightened. Popliteus tendinitis is a condition where the popliteus tendon, which runs along the back of the knee, becomes inflamed or strained. This can cause pain in the back of the knee, especially when bending or turning the leg. A meniscus tear is a tear in one of the two pieces of cartilage that act as cushions between the thigh bone and the shinbone in the knee joint. This can cause pain, especially with movement of the knee.