Typically, unembryonated eggs are passed in the human stool and become embryonated in the external environment ; after ingestion by freshwater fish, larvae hatch, penetrate the intestine, and migrate to the tissues .  Ingestion of raw or undercooked fish results in infection of the human host .  The adults of Capillaria philippinensis (males: 2.3 to 3.2 mm; females: 2.5 to 4.3 mm) reside in the human small intestine, where they burrow in the mucosa .  The females deposit unembryonated eggs.  Some of these become embryonated in the intestine, and release larvae that can cause autoinfection.  This leads to hyperinfection (a massive number of adult worms) .  Capillaria philippinesis is currently considered a parasite of fish eating birds, which seem to be the natural definitive host .

Capillaria hepatica adult worms reside in the liver of various animals, especially rats.  The females produce eggs that are retained in the liver parenchyma.  When the infected animal is eaten by another animal, the eggs are released by digestion, excreted in the feces of the second animal, and become embryonated in the soil.  Alternately, the eggs can be released following the death and decomposition of the first animal, and mature in the soil.  Following ingestion by a subsequent host, these infective eggs release larvae in the intestine that migrate through the portal circulation to the liver, where they develop into adults.

Capillaria aerophila adult worms reside in the epithelium of the tracheo-bronchial tract of various animals.  Eggs are produced, coughed up, swallowed by the animal, and excreted in its feces.  The eggs become embryonated in the soil.  Ingestion of infective eggs completes the cycle.  Transport or paratenic hosts may also intervene in the cycle.