Pentamidine isethionate salt is primarily used as an antimicrobial agent, particularly in the treatment of parasitic infections. It is highly effective against Pneumocystis jirovecii, a fungus that causes Pneumocystis pneumonia (PCP), a serious condition often seen in immunocompromised patients, such as those with HIV/AIDS. The drug is administered via inhalation or intravenous injection, depending on the severity and type of infection.

In addition to its use for PCP, pentamidine isethionate is also employed in the treatment of certain tropical diseases, such as leishmaniasis and African trypanosomiasis (sleeping sickness). For leishmaniasis, it is particularly useful in cases where other treatments, like antimonials, are ineffective or contraindicated. In African trypanosomiasis, it targets the early stages of the disease caused by Trypanosoma brucei gambiense.

The drug is also used prophylactically to prevent PCP in high-risk individuals, such as those undergoing immunosuppressive therapy or organ transplantation. However, its use requires careful monitoring due to potential side effects, including kidney toxicity, hypoglycemia, and hypotension. Despite these risks, pentamidine remains a critical therapeutic option in managing these life-threatening infections.