I have experienced the same thing with my 6 year old son. I think it is very natural for that age group, and even younger, and for the age group, it is not necessarily a sexual thing. As early as 12 months old, my son began touching and pulling at his penis during diaper changes and bath time, etc. From what I have read, it is normal for children to familiarize themselves with their anatomy, so there is really nothing to be concerned about.
The main things to focus on, in your appraoch to "dealing with" it, are: Teach him the correct terminology for his body parts, if you haven't already. Second, make sure he understands that it is okay to touch himself, and there is absolutely nothing to be ashamed or embarrassed about, but it is something he has to do in private--bedroom with door closed--and make sure you knock before entering to allow him privacy. Make sure he understands why his "private parts" are supposed to remain private. If you ask him why he rubs his penis, he will likely tell you that he does it because it feels good. That is the exact reason that a child "masturbates", it feels good. I relate it to a baby soothed by sucking on a pacifier or bottle. Also, it may now be time to answer any questions your child may have about his private parts or whatever else he may be curious about, but be sure to read up on the best way to answer those questions for his age. Kids age 5-7 take things very literally, so any form of run around will confuse them. It's best to remain factual but simple for the best understanding. And remember, There is absolutely nothing wrong with your child and make sure you make that very clear to him while discussing these topics. Just tell him that you are trying to teach him things and make sure that he understands and has the ability to ask any questions he has. Another important thing is to make sure your child knows that he can ask you anything, tell you anything and trust that you will not get upset or make him feel embarrassed. Building that relationship with your chils is very important. If anything were to happen to your child that he feels is inapporopriate or makes him feel uncomfortable, he will know that he can talk to you about it--and this is crucial. Once you have discussed what is appropriate and inappropriate with your child, you want to know that if something inappropriate happens, that he will tell you so you can keep him safe/protect him from adults and even other children from abusing him sexually or even emotionally.
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