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This happened to my daughter and she was diagnosed with a milk protein allergy. Are you BF or FF? If breast you may have to eliminate dairy to see if that helps. If FF there are hypoallergenic formulas out there. I would put another call out to your pedi and let him know that it's persisting.

DS had this with Microscopic blood also. It was MSPI, he's also a reflux baby and would scream non stop for hours his first 6 weeks. I don't know which really caused the screaming because he was put on special formula (alimentum) and Nexium at the same time at 3 months now he's doing waaayyy better. Definitly sounds like textbook milk protein intolerance.

My ped was more concerned with her behavior. Because my daughter was acting totally happy and normal, he said to not worry about it. But if she started acting colicky or seemed to be in pain, then we can try something. But for us it never progressed further than mucous and green stool (no pain or blood, etc.).

For us it was a symptom of mspi (well actually he is intolerant to way more than just milk and soy but those are the worst). Our GI doesn't really care too much about mucus unless it's pretty bad. He said it's a sign of inflammation/reaction. My son's diapers looked like they were full of chewed bubblegum and snot- like when I pulled the diaper away from his bottom there were thick strands of mucus.

But we also had visible blood and other symptoms- very severe reflux and vomiting unresponsive to meds. Oh yeah, and inconsolable screaming.

I've been on a strict elimination diet since September.