Recently, infection transmission risk associated with contaminated, patient-ready flexible endoscopes has attracted attention. Outbreaks of multidrug-resistant organisms resulting in infection and/or colonization have been particularly concerning. Recent CDC and FDA recommendations focus on reducing “exogenous” infection transmission and specifically recommend that endoscopy sites have quality systems in place for endoscope reprocessing. Another key recommendation is the culture of patient-ready endoscopes to detect contamination with organisms of concern. Remaining gaps in the guidelines include ensuring that optimal endoscope-channel sample methods are used and ensuring effective root-cause analysis and remediation when contamination is detected. In this review, we summarize the critical aspects of endoscope sample collection and present a practical approach to root-cause analysis and remedial action plans.