To diagnose digestive system problems, it's best to request a stool sample be examined under a microscope. It's possible that the mucous has been caused by something in your son's diet ... does it still occur?

Passing stool with visible mucus can be from a variety of problems. The best thing to do if you think your son needs medical attention is to take him to the doctor. Here is a link to more information.

http://ibdcrohns.about.com/od/relatedcondi tions/f/mucusstool.htm

I have a 3 year old girl. In feb. of 09 she had salmonella she was out for 3 weeks she was in hospital for 1 week its now almost 3 1/2 months later. She is constipated for 2 weeks and she is taking so med. that the doc proscribed and is still having problems. She is also having a lot of mucus in her stool. she still complains that her stomach hurts when she is going to the potty and she will start to cry because it hurts and wont come out. what do i do?

look up natural constipation cures , ultimately she has a inbalance in the digestive tract & she needs to hydrate better.
hope this is of some help!