Pentamidine isethionate is a drug primarily given for prevention and treatment of Pneumocystis carinii pneumonia (PCP), a type of pneumonia often seen in people with HIV infection. There are significant numbers of HIV patients who are allergic to or cannot tolerate Bactrim, the first line drug for treatment of PCP for which pentamidine can be useful. For prophylaxis against PCP, a second line drug often used for patients allergic to Bactrim is Dapsone. Monthly nebulised pentamidine is recommended for patients allergic to both Bactrim and Dapsone.

For treatment of PCP, 4mg of Pentamidine per kg of body weight is given intravenously once daily for 14 to 21 days. An aerosolized form given by nebuliser once monthly for PCP prophylaxis in those at risk.

The medication is also useful in Leishmaniasis and in prophylaxis against sleeping sickness caused by Trypanosoma gambiense . The exact nature of its antiprotozoal action is unknown. Hydration before treatment lessens the incidence and severity of side effects, which include liver or kidney dysfunction, hypertension, hypotension, hypoglycemia, hypocalemia, leukopenia, thrombcytopenia, anemia, and allergic reaction. It is generally well-tolerated.