Post-surgical endophthalmitis is a serious vision-threatening inflammation following any ocular procedure. Detection of endophthalmitis with culture has been traditionally used; however, endophthalmitis caused by viruses are overlooked. In a 1995 Endophthalmitis Vitrectomy Study by RK Forster, 33% of patient samples were culture negative. This represents a significant portion of patients who could have had endophthalmitis due to viruses. Using alternative techniques, we can characterize viral pathogens found in post-surgical endophthalmitis with qPCR (quantitative polymerase chain reaction) and polymerase chain reaction (PCR). qPCR quantifies the number of viral DNA strands whereas PCR indicates presence or absence of the viral DNA. This allows doctors to treat more patients which would have been previously thought to not have endophthalmitis. Patients diagnosed with endophthalmitis following intraocular procedures were recruited from Wills Eye Hospital and University of Washington from Sept 1st , 2014 to Dec 31st , 2015. All patients underwent vitreous or aqueous tap. The specimens were sent for microbial culture. Following DNA extraction, qPCR for Torque Teno Virus (TTV), Merkel Cell Polyomavirus (MCV), and actin were performed in all samples. qPCR results were verified via PCR and gel electrophoresis. A total of 29 samples were collected (12 culture-positive [41.38%], 17 culture-negative [58.62%]). Overall, 18 (62.07%) samples were positive for TTV and 15 (51.72%) for MCV. The presence of TTV or MCV was not associated with culture positivity by Fisher’s exact test. Viral DNA sequences are unexpectedly common in endophthalmitis. The role of these viruses in this disease process remains unclear.