The medial compartment is that part of the knee where the femur articulates with the tibia - but referring only to the inner or medial side.
The knee is considered to have three compartments - the medial compartment, the lateral compartment and the patellofemoral compartment. Arthritis and other conditions may affect only one of the compartments.
Knee stabilization in patients with medial compartment knee osteoarthritis. Lewek MD, Ramsey DK, Snyder-Mackler L and Rudolph KS. Arthritis Rheum. 2005 Sep; 52(9): 2845–2853.