The "clipless" pedal system got it's name because it replaced the toe clips and straps traditionally used by cyclists. Clipless pedals and bicycle shoes are ubiquitous in almost every segment of cycling, from professional racing to mountain biking. This is for a good reason -- being clipped to your pedals lets you transfer more power to your drivetrain without slipping off the pedal or losing your cadence. Clipless cycling shoes make you more efficient, but can be detrimental if you have your feet clipped in incorrectly. Getting your cycling shoes lined up properly can help you maximize your efficiency in the saddle.
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Clipping In With Clipless
Clipless pedals come in several varieties, which are adjusted in different ways. For casual cycling shoes and mountain bike cycling shoes, the SPD 2-hole system is the most popular. It uses a single contact point at the ball of your foot that corresponds to a metal cleat on the bottom of your cycling shoe, and can be readjusted by tightening or loosening the two bolts that hold the cleat to the plastic last in the shoe. The Look pedal system uses a three-hole system, which places another contact point toward the center of your foot. It is popular among racing cyclists since it redistributes the pressure from your feet over a larger surface area, making your stroke slightly more efficient. A third contact point means they'll need to be adjusted differently from SPD pedals.
Get In The Saddle
Before you can check the alignment of your clipless pedals, you'll need to make sure your seat is high enough for a proper pedaling stroke. With the bike leaned up against a wall, mount the bike and clip into your pedals, dropping one foot down to the lowest point in your pedaling stroke. At this position, your knee should be just slightly bent. Setting your seat at the correct height eliminates knee soreness from over-extending or under-extending your leg while pedaling.
Once you've got your seat height set, you can adjust the bolts on your SPD or Look pedals to re-position your foot on the pedal. Ideally, you want your foot and your thigh to be perfectly parallel with each other. If your foot or leg is twisted outward or inward, you'll lose efficiency. Set the cleat so that your legs line up straight, and are parallel to the top tube of your bicycle. This puts the power in your quadriceps directly over your foot, giving you maximum power with every downstroke.
You can diagnose an incorrectly placed bike shoe or a problem with your pedaling stroke visually, or by the amount of soreness you feel. If your knees or feet are pointed outward, it's time for a readjustment. Any rubbing between your crank and the heel of your cycling shoe can also indicate an improperly placed shoe. Soreness in the knees is the biggest indicator of an incorrectly placed foot or an improper seat height. You could be twisting slightly at the knee joint, and a seat position that is too low will be much harder on your knees over longer rides. Assume a straight position and use the proper seat height, and the soreness should correct itself.