My son had mucus in his BMs too. It was terrible and really worried me, but the doctors (pediatrician and GI specialist) weren't concerned. They said that it just means that his stomach was a little upset. My son has reflux, plus the milk and soy protein intolerence. Who knows if they were connected. Once he got off of formula (he was on special formula too) and on to Lactaid milk at 12 months, it went away. The doctors said that mucus doesn't bother them; blood in the BMs is what they look for.