Green poop may be normal for your baby. If your baby frequently has a green poo or yellowy green poo but is gaining weight well and is happy and content, it may just be normal for your baby. Causes of Green Poop may include Lactose overload, Not enough milk, An allergy to something in mother’s diet, baby tummy upset, Something green in mother’s diet, Teething and Some antibiotics or other medications may cause poop to rush through the bowel more quickly causing green nappies.