Inadequate absorption of the fat-soluble vitamins—A, D, E, and K—may lead to night blindness, rickets, anemia, and bleeding disorders. In about 20% of untreated infants and toddlers, the lining of the rectum protrudes through the anus, a condition called rectal prolapse. Infants with cystic fibrosis who have been fed soy protein formula or breast milk may develop anemia and swelling of the extremities, because they are not absorbing enough protein.

Complications in adolescents and adults with cystic fibrosis include a rupture of the small air sacs of the lung (alveoli) into the pleural space (the space between the lung and chest wall). This rupture can allow air to enter into this space (pneumothorax), which collapses the lung. Other complications include heart failure and massive or recurrent bleeding in the lungs.

About 15% of adults with cystic fibrosis develop insulin dependent diabetes because the scarred pancreas can no longer produce enough insulin. The blockage of bile ducts by thick secretions can lead to inflammation of the liver and eventually to scarring of the liver (cirrhosis) in about 5% of adults with cystic fibrosis. Cirrhosis may increase the pressure in the veins entering the liver (portal hypertension), leading to enlarged, fragile veins at the lower end of the esophagus (esophageal varices), which can rupture and bleed profusely. In almost all people with cystic fibrosis, the gallbladder is small and filled with thick bile and does not function well. About 10% of people develop gallstones, but only a small percentage develop symptoms. Surgical removal of the gallbladder is rarely needed.

People with cystic fibrosis often have impaired reproductive function. Almost all men have a low sperm count (which makes them sterile) because one of the ducts of the testis (the vas deferens) has developed abnormally and blocks the passage of sperm. In women, cervical secretions are too thick, causing decreased fertility. Otherwise, sexual function is not affected. Women with cystic fibrosis have a higher likelihood of complications during pregnancy (such as developing a lung infection or diabetes), but many women with cystic fibrosis have given birth.

Other complications may include arthritis, kidney stones, and inflammation of the blood vessels (vasculitis).