Tonsils. Artwork of a section through the mouth showing a palatine tonsil. The clear rod points to the tonsillar fossa, a depression that is occupied by a palatine tonsil (round, right). Tonsils are masses of lymphoid tissue and are part of the immune system. It is thought the palatine tonsils, found on either side of the throat, protect against respiratory tract infections. The large red mass that occupies most of the oral cavity is the tongue. At top are the soft (red) and hard (yellow) palates, which separate the oral cavity from the nasal cavity. The soft palate ends in the uvula, the little piece of flesh that hangs down at the back of the mouth.