Pitted tonsils are also referred to as cryptic tonsils. Tonsils are located on the back of the throat and typically have a smooth surface. Occasionally these tonsils will not be smooth but have have pitted holes. People that have pitted tonsils are more prone to having bacterial infections and strep throat because bacteria gets caught in the holes. To keep the tonsils healthy, it is important to rinse the mouth regularly with salt water and using antibacterial rinses.