Getting your eyes over the golf ball in your setup promotes a number of benefits that improve your address position and putting stroke. It also gives you a more accurate perspective of your target line, giving you the best probability of being aligned properly so you can focus on stroke and speed.
Having your eyes positioned directly over the golf ball accomplishes three things. First, your head and body fall into the proper position at address. Next, the ideal distance to the ball is established and this ensures that your arms sit close to your body creating a strong connection. Finally, with the body now aligned properly (head positioned with eyes over the ball and standing at the correct distance) the proper posture is promoted to allow the upper body to rotate independently of the head and lower body helping the putter stay on plane.
By being positioned with your eyes directly over the ball you will also see the target line without the influence of any optical illusions. Whereas, if your eyes are too far outside the target line, the line may appear to veer to the left, making you subconsciously aim too far right and if the eyes are too far inside the target line, the line may appear to veer to the right making you subconsciously aim too far left.
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Until now, the only way to know if your eyes were over the ball was to get into your putting setup and drop a golf ball from between your eyes to see if it lands on top of your ball. Check out the Eye it Up Visual Putting Aid at http://www.skilledgolfer.com for a more practical way to accomplish this. Get one and you'll be well on your way to holing more putts!