Introduction Pneumocystis jirovecii is an uncommon life threatening infection with a predilection towards immune compromised individuals. The National Comprehensive Cancer Network guidelines recommend anti-Pneumocystis prophylaxis in all hematopoietic stem cell transplant (HCT) patients. Trimethoprim-sulfamethoxazole (TMP-SMX) is a category 1 recommendation due to its significant reduction in Pneumocystis pneumonia (PCP) occurrence and related mortality, as well as its activity against other infectious agents, such as Nocardia. Objectives A retrospective chart review was performed to assess if our medical center's practice aligned with the standard guidelines for PCP prophylaxis in HCT patients. We aimed to identify factors contributing to deviation from guidelines as potential targets for process interventions. Methods Chart review was performed on all patients who received a stem cell transplant from 2011 to 2017. Information collected included: type of PCP prophylaxis, factors contributing to use of alternative therapy, breakthrough cases of Pneumocystis jirovecci or other infections. Results Of 204 charts reviewed, 11 were excluded due to early death. Most patients 85% (n=165) received TMP-SMX, 14.5% (n=27) received alternative therapy and 0.5% (n=1) received no prophylaxis. Reasons for alternative therapy included: allergy/intolerance, pancytopenia, renal insufficiency and elevated liver enzymes. There were no breakthrough cases of PCP. There were two breakthrough cases of Nocardia in patients not receiving TMP-SMX and a single case where a patient did not receive PCP prophylaxis due to miscommunication between the transplant physician and the primary oncologist. Conclusion Over the past several years there has been a trend towards choosing alternative agents, especially in the allogenic population, without impacting the incidence of PCP. However, there were two cases of breakthrough Nocardia when alternative agents were used. Development of a checklist, which outlines antibiotic prophylaxis and duration of treatment, may enhance communication between the transplant physician, primary oncologist and medical team.