A Sydney sheikh has appeared in court in relation to the alleged genital mutilation of two children.

Sheikh Shabbir Vaziri, 56, who police sources say is part of a lesser-known branch of Islam, has been charged with two counts of accessory after the fact of female genital mutilation and hindering investigation of a serious indictable offence.

Police will allege the two girls had the procedure, which is also known as female circumcision, performed on them in NSW when they were aged six and seven within the past 18 months.

Police allege one mutilation was performed in Sydney; the other in another metropolitan area.

Mr Vaziri, who was arrested today, appeared in Burwood Local Court this afternoon and was granted bail.