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In children, smelly breath that persists throughout the day is most often the result of mouth-breathing, which dries out the mouth and allows the bacteria to grow. Children who consistently breathe through their mouths might have colds, sinus infections, allergies, or enlarged tonsils or adenoids blocking the nasal passages, so a visit to the pediatrician is in order. Thumbsucking or sucking on a blanket can also dry out the mouth.
Here is a list of some very uncommon, but telltale, odors (mostly from Mace, Goodman, Centerwall, et al: The child with an unusual odor. Clinical Pediatrics 15:57-62, 1976). Take a whiff:
Three-year-olds often stuff items in their noses, and then forget about them. When my son Kevin was three, he put five peas up his nose before anyone found out! Watch for the combination of smelly breath and a smelly, yellow nasal discharge -- especially from one nostril. You and I might not think of stuffing peas up our noses, but three-year-olds think outside the box!