Pentamidine isethionate is a drug given for prevention and treatment of Pneumocystis carinii pneumonia (PCP), a type of pneumonia often seen in people with HIV infection. Although the recommended first line treatment for PCP pneumonia is trimethoprim combined with sulfamethoxazole (marketed in fixed combination as Bactrim), there are significant numbers of patients who are allergic to, or otherwise cannot tolerate Bactrim, for whom pentamidine may be useful.
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.