Padmasana can cause various problems for yoga practitioners. Meniscus tears usually occur as a result of falls and accidents but in yoga they can be caused by incorrect functioning of the Popliteus and Semimembranosus (inner hamstring). Both of these muscles control rotational forces in the leg. The Popliteus muscle retracts the lateral meniscus, while the Semimembranosus retracts the medial meniscus, preventing the meniscus from being compressed and torn when the knee is flexed. Swelling or pain in this area can cause muscular inhibition, making the meniscus vulnerable to injury.
Rotational forces are controlled by the hips and if the hips are unstable, you get incorrect functioning of the muscles around the knee, or overactivity of the hip flexors, causing internal rotation, which is problematic in Padmasana, because it requires external rotation at the hip.
Padmasana can also strain or overstretch the supporting ligaments at the side of the knee, more so when in asanas like Baddha Padmasana. People with longer, slender limbs have fewer problems because the length of the leg creates a smaller angle at the knee.
Sitting in Padmasana for long periods if you have shorter limbs is not a good idea, it is better for the knees to use Siddhasana when meditating.
Reading sources:
Ellenbecker, De Carlo, DeRosa, 2009, Effective Functional Progressions in Sport Rehabilitation
Sharkey, 2008, The Concise Book of Neuromuscular Therapy
Sports Injury Bulletin: Popliteus
Yoga Anatomy for the Perplexed 
If my knees are already injured (although not too bad, just light pain) due to too much sitting cross-legged, how can I help them heal as fast as possible besides avoiding sitting cross-legged?
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By cross-legged i dont mean padmasana, just regular cross-legged. I’m just a square one beginner at yoga. I moved to india 3 months ago and have been sitting cross-legged as much as possible in hopes of gaining some preliminary hip flexibility, but alas, my knees apparently took a beating just from that. It is a huge change though, from always sitting in chairs back home to most of the time cross-legged here…
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Hi Francisco
Thanks for adding some detail. Sitting cross-legged is a big adjustment if you aren’t used to it. Your knees are probably taking strain because your hip and leg muscles are tight so I suggest you work on dynamic hip flexibility while standing one one leg and stretching your adductor muscles first before you start bending your knees or putting weight on them. Some suggestions:
Standing on one leg, keeping your hips level, your torso straight: without leaning backwards or to the sides, bend your knee and bring it to hip height, or as high as you can manage. Draw circles in the air with your knee, keeping your body as still as possible, so that the movement is coming from your hip-joint. Make the circles in both clock-wise and anti-clock-wise directions. As you get stronger and loosen up, the circles will get bigger and bigger
Stretch your adductor muscles when your body is warmed-up from exercise by either:
1. lying on your back with your legs against a wall and opening your legs as far apart as they will go and keeping them in that position for 20-30 seconds, resting and repeating the stretch 3-4 times, or
2. open your legs as wide as they will go while seated on the floor, and keep them in that position for 20-30 secs, also repeating a few times. Don’t try bending forward until you are more flexible, that will strain your lower back
Stretch your Quadriceps muscles by standing on one leg and trying to pull your heel to your butt. Don’t allow your pelvis to tilt forward as you do that. Yoga classes will give you plenty of hip and hamstring stretches.
The golden rule with knees is not to do movements which cause you pain. Be patient but persistent and your body will loosen up.
I hope that works for you, feel free to let met know if it does or doesn’t.
Niki
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Dear Niki
My knees do not hurt but they make noises! A creaking sound when I bend them. I have started to be more careful in for example maricasana b and d, and also padmasana. Do you have any other tips for me? Is this something I should worry about? I love my yoga!
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Hi Nastassia
When knees creak a lot, it can be because the kneecap is tracking incorrectly in its groove. This is often caused by problems with the hip muscles that stabilise the knee and I suggest that you see a therapist to get your hip muscles assessed.
Niki
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