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What do you mean I shouldn't do that exercise?!

Why do you exercise?
To lose 10 lbs? To have energy to play with your kids? To get that summer beach body?
Whatever your personal reason is for working out there is one thing that is for certain. We exercise to improve our overall health. Now with that in mind.
If I gave you two exercise options, both with very similar benefits, but one of these exercise may potentially injure you, which one would you choose? No brainer, right? That is what is called a "contraindicated exercise".
Contraindicated exercises are those that have the potential to be detrimental to your health or physical well-being. Some exercises are labeled as contraindicated for general populations while others are contraindicated on a case by case basis due to a number of causes and limitations.
So lets break down the different types of exercise contraindications or the reasons why your trainer might not want you to perform a specific exercise.

Cardiac Limitations
So early in my career as a personal trainer I had the opportunity to work with a man who had recently come out of cardiac rehab and was cleared by his physician for "very light" cardio. After speaking with him a bit I learned that he had only 3/4 of his heart, a quarter had been removed during surgery. What this meant was I needed to challenge him without letting his heart rate get above a specific beats per minute or he would experience brain damage due to a lack of oxygen to his brain. 
So what did I do?
Well in this instance nearly every single cardio machine in the gym was "contraindicated" for this client due to his cardiac limitations. I decided to put him on a recumbent cycle and watched his heart monitor like a hawk. It turned out that this was the perfect fit for his current fitness level.
Many cardiac patients will have significant restrictions on their therapy and training. The goal being to gradually increase both duration and intensity of exercise to strengthen the heart without causing it stress. Not following these guidelines can result in another cardiac episode or even death.

Range of Motion
With an injury it is common for your range of motion to be restricted, after treatment your doctor will clearly outline any restraints that they've placed on you. Recently I worked with a client who was released from physical therapy and cleared for exercise. She was recovering from a shoulder surgery so her range of motion was extremely limited in one shoulder. Had she been doing her prescribed range of motion exercises solo she would have been cheating and moving through her spine but because she had a trained pair of eyes watching her move we have slowly begun to get her movement back. Working with a physical therapist or personal trainer can be helpful to teach you how to conduct your range of motion properly and how to adapt day to day activities to stay within that range of motion to prevent further injury.

Weight Bearing
If your limb is immobilized due to a cast, brace, or sling your ability to exercise and bear weight on that limb will be limited. If your limb is non-weight bearing you won't be able to even move the affected limb until your doctor says otherwise. Once you are told by your doctor or physical therapist that you are ready for partial weight-bearing activity you will begin with extremely light weight exercises.
You know those little 3lb. and 5lb. dumbbells sitting on the rack at your gym you joke about? That is exactly what those are for. When you are first released to exercise by your doctor you will be unable to lift heavy weight without the risk of re-injury. In order to progress you safely back to where you were before you were injured requires starting light and working your way to heavier weights over time with proper exercise programming. Going heavier on your exercises than prescribed can result in delayed recovery time and even further injury.

Exercise Specific
Exercise and movement science is still young. I mean just look 20 or 30 years back at the trends and studies (or lack there of...) compared to where we are now and you can see how far we have come in a very short amount of time. With that being said, it is very common that the exercise community learns something new that debunks something we previously believed was true. It is also common to find that a number of the exercises your "Old School" coach or trainer may have you doing could put you at a risk of injury.
As a trainer when I prescribe exercises to a client one of the very first things I think of is injury prevention. I weigh each exercise on a risk to reward scale, i.e. what will this exercise DO for my client and what are the potential RISKS associated with this exercise based on my client specifically. For example if my client has shoulder impingement issues I will choose to steer away from something like a upright row or an Arnold press. Likewise if my client has spine issues or disc compression I will avoid spinal flexion or something like a back squat. So in those cases the contraindicated exercise are client specific. There are also those times that the exercise science community realizes that an exercise just has too much risk compared to the potential benefits: full sit-ups, partner leg throws, inverted neck stands, etc.

Everyone is different.
Listen, if an exercise doesn't feel right for you or causes pain then just don't do it. One of the signs of a good trainer is the ability to modify an exercise on the spot for a client, by either progressing the exercise (making it more difficult) or regressing the exercise (making it easier.) If there is an exercise that doesn't work for you and your trainer tells you there isn't another option then the fact is they are just not thinking hard enough. There is always another option.

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