I've been biking since 2012. More seriously since last year. I bought new shoes (Sidi SPD-SL) last year. I did not have this with SPD and last year neither. In fact, I first had this pain last Tuesday. The following day I still had the pain during my commuting trip (5 km). Today, I did 75 km and it was quite hard to keep going at ~55 km so it does not happen right in. I checked the height of my saddle, my leg angle is about 150 degree and the cleat is properly aligned with the front of the knee (using a string with a lead). I tried different cleat position but I guess the injury was already done so it didn't help much. Is this the symptom of a specific thing? Big deal breaker... it's like in the front of the left knee, always the same leg.

You need go to doctor. Anyway.

I'd go to a physiotherapist. In fact I did, and it fixed the problem.

When I first went clipless I experienced knee pain too. I tried my level best to get SPD to work and I couldn't. I went with Crank Brothers which had more float and the pain went away. You know, sometimes we talk about bicycling and set-up as if it were an exacting science. It's not. We are all unique. As crazy as this sounds, try some platforms for a few rides and see what happens.

Sounds like you didn't change your shoes or cleats. If you were riding a lot last year, without pain, and now you have pain of recent and abrupt onset, you should look very carefully at what changed last Tuesday. Did you make any adjustment? Was this a significant step up in your riding distance?

I recently had knee pain after a long (for me) ride, the second longest ride I'd ever done. I found the problems was that during the ride my seat post had slipped down almost a cm. I need a fair amount of leg extension, and that was enough, over the longer distance. So look hard at what changed last Tuesday. And you'll need to recover, now that it's injured, as you said.

Could be lots of things, inflamed fat pad, tendonitis, poorly tracking kneecap, chondromalacia...

Doc will take an x-ray, guess, tell you to rest.

It probably won't help once you resume.

Then they might order an MRI, which is a better diagnostic.

Personally, what helped my knee is specific stretching, daily use of Penetrex, swapping out my road double for a compact.

It's been 18 months, and I'm finally able to push hard in the mountains again.

What ruins my knee is regular use of ibuprofen, advil, aleve, or any pain reliever. It seems to impair healing and recovery after riding. Everyone is different though.

Have you been off the bike for a while, then just hopped on and the knee decided to act up? Is it "a lot" or just "a little"?

I've had my knee act up a bit, but I think it's overuse. Comes and goes, which makes me think I'm on the right track. Dialing back my power has helped (I was pounding away to keep up on group rides).

From what I've read, front of knee means seat too low; but then again, left side only means your body is trying to accommodate for something else. You could try reading Steve Hogg's stuff, it might help.

I have a cranky right knee that I also had years ago playing tennis. It is probably best if you seek professional help. It may be that just a professional bike fit is all you need. It will be helpful if you pay close attention to your pedaling movement. In my case, I noticed the knee would flop to the inside, occasional brushing the top tube. I added a 1 degree shim under the cleat and built up the arch support in the right shoe, all of which keeps the knee moving straight up and down with little inward flop. I further do knee exercises to strengthen the knees.

My knee problem is due to some trauma suffered in earlier years but I seem to have dealt with it successfully. If your knee does not have serious structural problems, it may be a bike fitter will help you. This is why I suggest you pay close attention to how you pedal. To paraphrase that great American philosopher, Yogi Berra, you can tell a lot by observing. I watch cyclists on the bike path here with legs and knees flying every which way and marvel those knees don't disintegrate before my eyes.

I'll suggest it once more.

Don't go to a doctor, he doesn't have the knowledge to help you cure something like that. A physiotherapist does have that knowledge. He won't order an mri or any of that stuff, unless he suspects something is broken.

Any chance it is unrelated to cycling at all?

Pains can be odd. I aggravated an old hockey injury last weekend while cycling, which I, at the time, attributed to trying out a new bike setup. Knee hurt like crazy most of the week, to the point where I almost skipped a 51 mile (already paid for) mass ride I had already signed up for this weekend. Woke up Saturday morning with some pain, just decided I'd ride and if it got bad enough I'd pull off and get picked up. Finished the ride on that same bike, went an additional 11 miles to make a metric century, and yesterday and today the knee has felt perfect.

Long story short, the issue wasn't at all what I was attributing it to.

Any doctor will just tell you to ride less.

I had knee pain a few years ago. What has helped me is cross training with running combined with lots of quad stretching/rolling. YMMV.

Thanks guys for the comments. To answer some questions, there are a couple of things that changed since last year when I didn't have this problem.
I increased the angle of the saddle and lowered the saddle to compensate. I think I also adjusted the saddle position so that my knee is lined with the middle of the cleat when the pedal is at 90 degrees.
Result: no more sore butt and I can finally keep going for long distance no problem until I get that damn knee pain.
I am training much more seriously and I might be stressing a bit more the knee joints so that might explain why... cleat position was also modified. Can't seem to find the right set-up. I always end up with something not quite perfect...
The physiotherapist suggestion is probably the best. I hope I'll find solution to my problem. Will look for some one who has some experience with cyclist.
I live in montreal if by chance anybody know some one around there, let me know!

This what I would do as well, ride with platforms for a week or so and see if anything changes for the better.

At the opposite extreme, switching to the red "zero float" (they really do have a considerable amount of float when shoe flex is considered) cured my knee problems.

We all have a unique geometry. Very subtle changes of cleat position can make a huge difference.

I took to marking the seat post and cleat location with a Sharpie after I found the sweet spot so I can get them back exactly the same.

IME, lowering the saddle will put more pressure on the knees, because the power stroke is reached when there is more bend in the leg.

Perhaps take a week off of the bike, and look for other exercises to fill in.

It is hard to say about float. Your SPD pedals had a little.. The SPD-SL allow using wedges and precise adjustment of angles.

Or, speedplay pedals are supposed to have lots of float.

A little float might help your legs move to their natural position. No float lets you force them into the optimal position.

Also, "flats" would allow you to push down without pulling up.

The "knee" is a complex mixture of bones, cartilage, tendons, and muscle. Try to pay attention to where it is hurting as that may also influence your decisions of how to work with it.

Also, does it hurt walking? Swelling?