Summary Background Appropriate endovaginal/rectal ultrasound transducer disinfection has been an ongoing and vexed question in gynaecology, obstetrics and urology. However, the routine use of probe covers followed by low-level disinfection (wipes/spray) is usually applied between patients in some countries (e.g. France). Aim To perform a systematic review and meta-analysis of the scientific literature in order to identify case reports of contamination following endovaginal/rectal probe use, and to estimate the infection prevalence related to the use of these probes in common daily practice. Methods Systematic review and meta-analysis. Results From the 867 potentially eligible references, 32 articles were finally included. Very few cases with an established route of contamination had been reported. Indeed, apart from occurrence of outbreaks, it is difficult if not impossible to detect viral contamination through the use of endovaginal/rectal ultrasound probes. However, there was a pooled prevalence of 12.9% (95% confidence interval: 1.7–24.3) for pathogenic bacteria, and 1.0% (0.0–10.0) for frequently occurring virus (human papillomavirus, herpes simplex virus, and cytomegalovirus) for endovaginal/rectal probes, both after low-level disinfection. The pooled prevalence of infected patients after transrectal ultrasound and guided biopsies was estimated to be 3.1% (1.6–4.3). Conclusions There appears to be a risk of transmitting bacterial or viral infections via endovaginal/rectal ultrasound transducer, and the present meta-analysis provides an estimate of this risk. Further research with sophisticated modelling is warranted to quantify the risk.