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.

Knee compartments
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.
-
-
CLINICAL PUBLICATIONS
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.