In the suppurative form, respiratory tract infection, allergic reaction, nasotracheal intubation, or positional changes allow nasopharyngeal flora to reflux through the eustachian tube and colonize the middle ear. Suppurative otitis media usually results from bacterial infection with pneumococci, Haemophilus influenzae (the most common cause in children younger than age 6), Moraxella catarrhalis, beta-hemolytic streptococci, staphylococci (most common cause in children age 6 or older), or gram-negative bacteria.

Predisposing factors include genetic factors, such as susceptibility to infection; the normally wider, shorter, more horizontal eustachian tubes and increased lymphoid tissue in children; and anatomic anomalies. Chronic suppurative otitis media results from inadequate treatment of acute otitis episodes or from infection by resistant strains of bacteria or, rarely, tuberculosis.

With secretory otitis media, obstruction of the eustachian tube causes a buildup of negative pressure in the middle ear that promotes transudation of sterile serous fluid from blood vessels in the membrane of the middle ear. Such effusion may be secondary to eustachian tube dysfunction from viral infection or allergy. It may also follow barotrauma (pressure injury caused by inability to equalize pressures between the environment and the middle ear), as can occur during rapid aircraft descent in a person with an upper respiratory tract infection or during rapid underwater ascent in scuba diving (barotitis media).

Chronic secretory otitis media follows persistent eustachian tube dysfunction from mechanical
obstruction (adenoidal tissue overgrowth, tumors), edema (allergic rhinitis, chronic sinus infection), or inadequate treatment of acute suppurative otitis media.