I agree that it can take a while for the cow's milk proteins to leave both mom 
and baby's system. I have read that 3 weeks is the "standard" time frame, but 
it could be longer - speaking from experience, I have a 13 month, breasfed 
daughter and we dealt with a similar situation. For her, it took about 5 to 6 
weeks for the felcks of blood to disappear. Every case is different. 

How are the stools otherwise? Just flecks of blood or are they mucousy? At 12 
weeks the gut still has a way to go to mature and could take longer to heal 
from the insult of the cow's milk protein.

There is an interesting article in the April 2006 volume of Pediatrics 
titled "Rectal Bleeding in Infancy" - research done in Finland abut the 
incidence of this. At the end of the article the researchers suggest the use of 
probiotics with infants who are experiencing rectal bleeding. They found that 
the infants who had flecks of blood in their stool tended to have low counts of 
bifidobacteria and lactobacilli compared to the control infants. Is this an 
option the mom has discussed with her pediatrician? Just make sure the 
probiotics she chooses are dairy free. 

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