By kk from CV
Be gentle and hold with one hand on underside behind front legs and one hand under the back legs and rump. If you leave thier feet dangle they think you are going to drop them. That causes them to wiggle, squirm, and fight, and you very well could drop the little piggie. A lot of guinea pigs never get over the running from you when you try to pick them up. They are small animals and think you are going to hurt them or eat them. It's a natural instinct. But they are usually fine after you catch them and pet them nicely for a while.
I got a guinea pig as a surprise present and I had the same problem. It took me about a week to get her comfortable with me but she still runs a bit when I try to pick her up. They never like being picked up but they can learn to enjoy being held. I give mine fresh fruits and veggies twice a day and talk to her a lot. She even responds to her name now! Just be super gentle when picking up your guinea pig and it will get used to being held eventually. Spoil it with fresh fruits and veggies and I promise it will love you forever!
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