As sex reassignment surgeries become common and advanced, doctors are more likely to encounter cases with 'different' anatomy. Due to variations in examination and management as compared with non-transsexual patients, these cases generally prove challenging to the physicians. We present a case of recurrent bacterial vaginosis (BV) of neovagina in a transsexual patient successfully managed by using metronidazole gel and occasional douching. This case illustrates the difference in the microscopy of vaginal flora and management of BV in transsexual as compared with non-transsexual women.