Pain felt at the outer or inner sides of the knees is often directly related to the hips and can have a variety of causes, which need to be assessed and treated by a specialist.
As explained in Knee Injury and Pain in Yoga, the Gluteus Medius stabilises the pelvis in a horizontal plane and when the Gluteus Medius is not functioning, other muscles take over. Hip stabilisation then occurs via the Tensor Fascia Latae (TFL) muscle, which is connected to the Iliotibial Band (ITB). The ITB attaches to the outer side of the knee and pain is felt there if the TFL is compensating for the Gluteus Medius. A physiotherapist may massage and stretch this for you but the problem always returns, because the hip muscles are functioning incorrectly and are the actual source of pain.
Pain in the inner side of the knee, below the kneecap is related because the Sartorius muscle attaches here and it also becomes overactive when hip stabiliser muscles don’t work as they should. It is relatively easy to spot malfunctioning hips in yoga: in standing balancing postures like Vrksasna or Utthita Hasta Padangustasana, the hip pushes out to the side and the pelvis tilts downwards and it is difficult for the person concerned to keep their pelvis level. The hips also usually feel painful and tight.
Teachers and students need to be aware of the importance of keeping the pelvis level during any asana practice- an inability to do so shows an existing problem but bad habits can also create the same problems over time. Hip problems like these can be effectively treated by a good Biokineticist, but if hips are not treated, lower back pain and Sacroiliac joint problems can develop.
Hip weakness also places rotational stress on the knees, Pain at the Kneecap and Knees and Padmasana will look at rotation in more detail. Another related article on this site: Lateral Pelvic Tilt in Yoga Practice
Reading sources: Ellenbecker, De Carlo, DeRosa, 2009, Effective Functional Progressions in Sport Rehabilitation De Franca, 1996, Pelvic Locomotor Dysfunction