Having had 3 kids with food allergies, I'd ask a few questions, especially since I've discovered how little many pediatricians seem to know about breastfeeding. How green is the poo? Grass green? Avocado green? Is there any mucous? By that, I mean does it stretch at all? Are there any othe red or black flecks? Does he have any other skin issues like eczema?
Green stools indicate that there is bile in the stool and that typically happens when the stool passes quickly through the intestine. This occasionally happens in normal breastfeeding and so an occasionaly green poop is OK. If they are consistantly green then it indicates that they are passing through quickly all the time, and this can be caused by a few different things.
Foremilk is watery to quench thirst and sweet while hindmilk is more fatty and sustaining. Too much lactose (milk sugar) can have a laxitive effect and cause gas, green frothy stools, more frequent demands for feeding and discomfort. If you have oversupply/overactive letdown baby may choke or gag while nursing, pull off the breast and you may notice that your milk squirts forcefully in several jets during letdown. (I could hit another kid sitting a distance away when baby pulled off ;)) You may also get engorged a lot, suffer plugged ducts, and find you have a hard time getting a breast truly "empty" or soft.
If there is mucous or blood in the stool it is a sign that the intestinal lining is irritated, probably due to a protein intollerance or allergy. Dairy is generally the first place to start, which means removing all traces of dairy protein from your diet--this means not just butter, milk, cheese, yoghurt, ice cream, etc but also anything containing casein, whey, lactose, and caseinates of all sorts. It can take a couple of weeks for the dairy to completely clear your system so be patient.
It's worth noting that baby can be senitive to any one of a number of proteins in your milk. For example, many babies who are sensitive to dairy are also sensitive to soy. Soy is highly allergenic, and in some cases soy sensitivity can extend to the whole legume family. Other common allergins include wheat, egg, fish, shellfish, citrus (including tomato), and nuts.
For many moms, removing dairy is enough, but you won't know unless you avoid all dairy-containing foods. It can be tricky: for example, non-dairy creamer is not dairy-free! But once you learn to read labels it gets easier.
If you have any questions, please feel from to email me. I have 3 kids, I've had oversupply-overactive letdown with all of them, and they each have different food sensitivities--I've seen a LOT of green poo!! In fact, I'm currently avoiding all dairy, soy, legumes, and gluten for my 7 mo old!
Good luck!