Background: Duodenoscope-emerging infection especially drug-resistant bacteria is considered a major concern nowadays. Different approaches were attempted to overcome this problem, like double high-level disinfection procedure. We performed a systematic review and meta-analysis to evaluate risk difference for positive cultures from duodenoscopes between double high-level disinfection (dHLD) and single (standard) high-level disinfection (sHLD). Main body: A thorough literature search (in October and November 2019) for studies comparing dHLD and sHLD for duodenoscopes was performed by 3 researchers in the Web of Science, Scopus, PubMed, and Cochran databases. The search terms were "duodenoscope," "ERCP endoscope," "disinfection," "sterilization," and "reprocessing," and only randomized clinical trials with the English language were accepted. Four trials were identified studying dHLD, and only 2 clinical trials comparing dHLD with standard sHLD were found reporting 6193 duodenoscope cultures. Overall sHLD cultures were 2972, and dHLD cultures were 3221; overall positive cultures were 140 in sHLD and 161 in dHLD. The results of a meta-analysis using the random-effect model showed no significant risk difference (RD) between the 2 procedures for duodenoscope positive cultures (p = 0.53, RD 0.003, 95% CI "− 0.007-0.013"). Conclusions: Double HLD offered no significant difference over single HLD for duodenoscope disinfection. An alternative strategy to overcome duodenoscope-transmitted infection is a big issue to be resolved.