As mentioned earlier, there are many pits on the surface of the tonsils. As we masticate the food, the salivary enzymes that act on food, break the food down. The bacteria that may be present in the oral cavity, act on the residue of the ingested food. These residues, along with mucus and dead cells, can sometimes, become lodged and harden in the form of tonsil stones in the pits present on the tonsils.