Abstract Introduction The presence of biofilm at the inflatable penile prosthesis (IPP) component sites, which resists eradication, likely increases postoperative infection rates in revision surgery. The microbiome of (IPP) revision surgery has been shown to be increasingly complex and the weak microbe Staph epidermidis is no longer prevailing and was previously considered the major causative agent for overt infections. Furthermore, next generation sequencing (MicrogenDx, Lubbock, TX, USA) has been used recently to demonstrate that in certain scenarios such as mechanical malfunction, erosion, and infection, specific microbes dominate. Due to the disastrous complications with postoperative IPP infection, it is paramount to provide additional evidence for increased utilization of next generation sequencing over traditional cultures during IPP revision surgery. This will serve to guide postoperative treatment if necessary. Objective We investigated a cohort of IPP revision patients receiving intraoperative low concentration chlorhexidine (CHG) lavage to see whether next generation sequencing or traditional cultures of the pump space reveals more isolates. Methods A total of 31 patients with indwelling IPPs underwent revision surgery for both infectious and noninfectious reasons between May 2021 and March 2022 by a single, high volume implant surgeon who solely uses 0.05% CHG dip and irrigation. Once the pump capsule was entered, swabs were taken from the pump space and sent for traditional culture and next generation sequencing. All cultures were obtained prior to irrigation with 0.05% chlorhexidine (CHG) solution (Irrimax corporation, Lawrenceville, GA, USA). All patients received perioperative clindamycin, gentamicin, and fluconazole. Results 1 patient was excluded due to missing next generation sequencing results. Of the 30 remaining patients, 4 presented with infectious and 26 with noninfectious etiologies. 93% (28/30) patients had negative traditional cultures prior to irrigation with 0.05% CHG; however, 21% (6/28) of these patients had isolates on next generation sequencing. Only 7% (2/30) had positive preop irrigation cultures and isolates on next generation sequencing. Both of these patients presented with infection. 1 of these patients had a concordant next generation sequencing result. However, the other patient had multiple isolates. The traditional culture showed only pseudomonas a. On NGS, it was the third most abundant on NGS at only 4% compared to the most and second most abundant being E. coli at 83% and Klebsiella p. at 12%. Conclusions These results suggests that a greater number of isolates are obtained using next generation sequencing compared to traditional cultures during IPP revision surgery. Consequently, this may lead to better prevention and/or better guide treatment of postoperative IPP infection in the setting of IPP replacement. Although, further studies are needed prior to universally adopting this modality. Disclosure Yes, this is sponsored by industry/sponsor: MicrogenDx. Clarification Industry funding only - investigator initiated and executed study. Any of the authors act as a consultant, employee or shareholder of an industry for: MicrogenDx.