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The Case for Free Weights
Free weights require you to stabilize and balance your body (using additional muscles), giving you a better workout in the same amount of time. You can also do a larger variety of exercises instead of being limited to the machines your gym has available. If you have a stronger side (for example, your right triceps group is stronger than your left), machines typically allow the dominant side to compensate for the weaker one. With free weights, you force the weaker muscle to do its share of the work. The negative of using free weights is that your risk of injury increases because it's easier to do exercises improperly. And because the number of exercises is endless, it's easy to create a program that's not balanced or omits exercises that target important muscle groups.
There are pros and cons to both machines and free weights, so a combination of the two can yield maximum results.
The choice to use machines or free weights is a very individual one and should be based on your overall goals, time available, experience, and injury history/risk. Here are some examples of how these variables will affect the types of exercises you might choose.
Experience: I tend to recommend that beginners use machines because you really can't go wrong with them. Machines make it easy for you to do exercises correctly. Another bonus is that you don't usually need help or a trainer to figure out how to set up and adjust a machine—they usually have instructions and pictures on them, and even tell you which muscles you're working.
General Fitness: Machines can give you a great foundation for general strength training, whether you're just starting out or aren't sure what your goals should be.
Functional Fitness: If you exercise to improve your ability to move and function in everyday life, then free weights will be a better choice because you can use them to mimic normal movement patterns, making them easier over time.
Muscle size and strength: Machines usually win in this case because they can really target and isolate a single muscle group while allowing you to lift more weight, which is crucial for developing size and strength. But ideally, a combination of free weights and machines will help build strength and size.
Specific fitness goals: The only way to get better at pull-ups is to do pull-ups. But if you're too weak to pull yourself up, an Assisted Pull-Ups Machine can help you get there. The point is that some machines can help you reach very specific fitness goals, such as this one.