I have bumped up our soreness thread so that you can give it a read, you might find some ideas in there.
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Originally Posted by Guadalupe 
his first infection I didn't even know what the problem was. I thought something terrible had happened. He was screaming and would collapse when he tried to walk and would kind of climb up me like he was trying to get away from the lower half of his body. I took him to the Dr and he didn't retract his foreskin, but kind of peered in the top of it, just exposing the tip of the penis, if that makes sense. He said it was inflamed and ulcerated.
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It makes perfect sense.
Quote:
Originally Posted by Guadalupe 
The second infection was similar and when i went to the Dr he examined him in the same way and when he touched his penis about half a teaspoon of puss (very similar in colour and consistency of green snot) came out.
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The puss could either be puss or smegma, when the foreskin separates from the glans it is not uncommon for a discharge as you describe. The way to know whether it is puss as in discharge from an infection is either testing or you can tell by the smell. He didn't have a fever did he?
Quote:
Originally Posted by Guadalupe 
He's not had a discharge like that since. At the moment the foreskin is reddened and his sleep very disturbed. I had to give him pain relief last night to get him to the point of not crying and saying "bottom hurts" "wee wee hurts". I have never seen him urinate, but i have no reason to believe it is painful (by "wee wee" I think he means "penis"). He has what I consider a good sized opening at the end of his foreskin. He is a very particular little thing and refuses to not wear a nappy.
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I am still thinking this is an unusually bad case of separation. I am hoping more posters will come along to give additional opinions. My best advice I believe is the baking soda baths, diaper free time, and the pain reliever you gave him is a good thought too.
While I am thinking of it, any changes in chemical use? Things such as soaps, detergents, ect? Has he been to a pool recently? Type of diapers? Sometimes these things can cause reactions. Just throwing it out.

Just out of curiosity, where are you posting from?
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