[1] In African trypanosomiasis it is used for early disease before central nervous system involvement, as a second line option to suramin.

[4] While the way the medication works is not entirely clear, it is believed to involve decreasing the production of DNA, RNA, and protein.

[15] The additional or sequential use of other nephrotoxic drugs like aminoglycosides, amphotericin B, capreomycin, colistin, polymyxin B, vancomycin, foscarnet, or cisplatin should be closely monitored, or whenever possible completely avoided.

However, pentamidine is suspected to work through various methods of interference of critical functions in DNA, RNA, phospholipid and protein synthesis.

[8][18] Pentamidine binds to adenine-thymine-rich regions of the Trypanosoma parasite DNA, forming a cross-link between two adenines four to five base pairs apart.

Similarly, pentamidine inhibits type II topoisomerase in the mitochondria of the Trypanosoma parasite, resulting in a broken and unreadable mitochondrial genome.

When inhaled through a nebulizer, pentamidine accumulates in the bronchoalveolar fluid of the lungs at a higher concentration compared to injections.

[18] Pentamidine isethionate for injection is commercially available as a lyophilized, white crystalline powder for reconstitution with sterile water or 5% Dextrose.

The sudden increase in requests for use of Pentamidine isethionate in then unlicensed form from the CDC in the early 1980s for treating Pneumocystis jirovecii in young male patients was key in identifying the emergence of the HIV/AIDS epidemic at that time.

[22] Its efficacy against Pneumocystis jirovecii was demonstrated in 1987, following its re-emergence on the drug market in 1984 in the current isethionate form.