I often write off the back of customer enquiries post-fit, when they leave, but are left with one of the concerns they had when arriving. I have a favourite quote, that I first heard from Nathan White of Cobra9 Cycling Podiatry – “If you are pain free, I can not make you more pain free”.
Especially when it comes to understanding feet, it is vert important to know when to fix something as preventative medicine, or accept that the imperfection actually IS the preventative medicine.

Ill focus on heel/crank rub in this article and try to explain that it could be both acceptable (or unavoidable) or unacceptable depending on the client.

Crank Rub the the obvious side effect of a heel rubbing against it during the pedal stroke, and usually means that the rider’s toes are pointing away from the bike. It can also mean that the entire foot is so close to the crank arm that it’s rubbing at the forefoot.
Determining where the shoe is contacting the crank is obvious based on where the rub mark is on the crank.
Investigating whether it is bilateral or unilateral (both feet or just one) and if the heel is inverted by the same margin on each side is where I begin from a diagnostic view point.
If it is unilateral, then we are looking for a different set of solvents than when it is bilateral. Often, unilateral foot misdirection is a component of pelvic dysfunction and leg length.

Bilateral is usually a component of Q factor or an obstacle that is forcing the legs out evenly each side (could be hip flexors, pregnancy, or misalignment with cleat lateral placement).

Heel rub in a bilateral form is actually a GOOD thing. Its not the best thing, but its not detrimental on its own.
It the hip and knee need to travel away from the bike because of an obstacle that can not be overcome through positioning, the heel moving toward the bike allows the knee to move away from the bike without twisting the knee. The ankle can do this movement well, as can the hip. If we decided to lock the foot straight, but the knee still needed to travel away from the body because of a pregnant belly, the knee would be the component that would have to twist. I’m not an orthopaedic surgeon, but I can tell you that knees don’t like to twist.
That is not to say that there arent other ways to reduce the distance the  knee travels away from the body, but in some circumstances its not entirely detrimental for the foot to be perfectly parallel with the bike.
I use a standard range of lateral travel (knee movement left to right) that I consider to be acceptable, but this is a massive topic that deserves its own article.

Unilateral dysfunction is much more of an issue, because there are many more components to resolve. This often comes with a significant leg length difference, or pelvic rotation that sends one leg away from the bike, and one toward the bike.
Clients with this sort of dysfunction usually present with knee pain and one sided back pain, and though the solutions are quite simple, they take time to reach a solution. Adaptation takes TIME. Though there is usually some instantaneous improvement, it often takes a couple of weeks or months to reach a complete solution.

I do use (and have used) cleat wedges, but its very rare for me to install them these days. If you have an actual FOOT issue, I will suggest that you either use some quality off the shelf shoe inserts, or some prescription orthotics suitable for cycling (different to your every day devices). Something I replace regularly are cleat wedges installed to try and deflect the knee back into the bike, when it is an obstruction or any number of hip issues. If you have had cleat wedges installed, I would be seeking an understanding as to why they are appropriate, and what the underlying problem really is.

Then there’s the muscular component that can lead to the knee lateral travel which can be easily assessed, but I would refer you on to a physio to seek resolution (another big topic).

It’s quite difficult to self diagnose which course of action is appropriate, as it is very difficult to see this relationship from on top of your bike. That’s where a visit to your local friendly fitter can be beneficial.

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