Objectives: The present study was performed by the aim of qualitative evaluation of the experience of parents from the prepubescent period of their children with gender identity disorder. Method: This study was a qualitative research. By the available and targeted method of sampling, 10 parents of children with gender identity disorder who were referred to Tehran Psychiatric Institute in 2012 participated in a deep unstructured interview. After typing, the recorded interviews were encoded by the method of inductive content analysis. Results: The gathered findings were classified in four main categories as “similarities to the opposite sex / differences from the same sex”, “difficulties in school”, “the way of coping with the reality of gender identity issues”, and  “parents’ feelings”. By the different ways, the parents had experienced the reality of the difficulties of gender identity in their child during his or her childhood, but they postponed coping with this event by using the various mechanisms such as negligence, overseeing, giving a promise, lack of seriously and procrastinating.  Conclusion: The present study is the first research in our country in which the parents of children with gender identity disorder demonstrated their problems. With consider to the obtained findings from the present study, it is necessary not only to design the multi-dimensional programs which educate general public (include parents) and also experts for becoming familiar with gender identity but also to involve the parents of children with gender identity disorder  in cooperation with primary healthcare providers for the process of diagnosis and treatment.