Background <p><i>Trichomonas vaginalis</i> is one of the most prevalent pathogens responsible for non-viral sexually transmitted infections. The infection mainly affects women of childbearing age, with the potential for complications during and after pregnancy. Although perinatal transmission is rare, it carries the risk of resulting in neonatal infections. To date, only a dozen documented cases have been reported in the scientific literature. Since modern PCR techniques is more sensitive than conventional methods, it can be anticipated that this microbe will be detected more frequently, even in newborns.</p> Case presentation <p>The present report describes the clinical courses of two neonates contaminated with <i>T. vaginalis</i> documented by multiplex PCR. The pathogens were detected in newborns without obvious clinical suspicion of sexually transmitted infections.</p> Conclusion <p><i>T.vaginalis</i> can be transmitted from an infected mother to her child during vaginal delivery resulting either in transient colonization or in manifest disease. It is likely that in the future, when multiplex PCR becomes more widely apllied, sexually transmitted infections will be detected more frequently in neonates.</p>