Trichomonas vaginalis is an anaerobic protozoan parasite of the human urogenital tract, and is sexually transmitted to over 170 million people worldwide each year. Although most infections go unnoticed, serious health implications include the increased transmission and acquisition rate of human immunodeficiency virus (HIV) and low infant birth weight. Drug resistance in T. vaginalis is an emerging and alarming predicament as only one drug, metronidazole, has been approved for treatment. Several gene families have been implicated in the development of derived drug resistance in T. vaginalis, however, very little is known about how this phenomenon arises in clinical samples.Genome plasticity is common in protists, and specific rearrangements, changes in ploidy and chromosome size are frequently correlated with drug-resistant phenotypes in other protozoan parasites. Limited genomic information is available for T. vaginalis due to an unusually large genome size and highly potent nucleases which confound modern molecular technologies. The present study aimed to investigate genome polymorphism using modified, traditional mammalian karyotyping techniques and a collection of five T. vaginalis strains varying in metronidazole susceptibility (including clinical and laboratory-derived resistance) and geographic sampling origin (Australia,