Branchial cleft cysts and sinus are congenital conditions (conditions present at birth) caused by unexpected changes during pregnancy. Often, these changes occur around the 5th week of pregnancy, when gill-like structures around the neck do not reabsorb back into the skin. At the same time, pharyngeal arches (bands of tissue that develop into the head and neck) start to form. Later, these arches become bone, cartilage, muscles and blood vessels. When these arches form incorrectly, they create empty spaces that fill with fluid and become cysts. Most of the time these conditions are unilateral (occur on one side of the neck). When branchial cleft cysts are bilateral (on both sides), your child is more likely to have other congenital abnormalities (conditions present at birth).