Trichomoniasis presents a broad spectrum of clinical patterns ranging from asymptomatic to severe vaginitis and cervicitis. Despite its importance, very little is known about the genetic relatedness of its causative agent, Trichomonas vaginalis, and the clinical phenotypes. To address this question, analysis of restriction length polymorphism (RFLP) within the intergenic spacer of the ribosomal DNA (IGS) from 60 clinically defined isolates of T. vaginalis was performed. This is the first description of the IGS polymorphism of T. vaginalis. As expected, a considerable number of patients were asymptomatic (28%) while only 12% presented both leukorrhea and macular colpitis, the most evident symptoms of trichomoniasis. The IGS-RFLP with the use of eight restriction enzymes showed absence of correlation between the genetic relatedness of the isolates and symptomatology. Further studies are necessary to evaluate the importance of the IGS polymorphism to the parasite virulence and clinical phenotype.