INTRODUCTION Congenital cholesteatoma is a rare entity, arising from aberrant epithelial remnants left at the time of closure of the neural groove between the third and fifth week of fetal life with incidence ranging from 4 to 24%. Congenital membranous atresia is more common on right side and unilateral presentation is a rarity in females which is seen in our case. Here we report a rare case of 44 year old female with bilateral hard of hearing which is more on right side with ear discharge and was diagnosed by CT scan to have congenital unilateral membranous atresia with rare finding of ossicular malrotation associated with congenital cholesteatoma which are extremely rare combination of findings in a single patient. Knowing such rarity may help in appropriate surgical approach when confronted with such cases in clinical practice.