Some looked like men but were actually women and vice-versa, he said.
"Their feelings are also different from their looks," he said at a press conference during the Kuala Lumpur Summit 2014 here Tuesday.
Dr Mahathir, who was asked to comment whether the Syariah and civil court judges should sit together to hear the cross dressing case, said it would be great to have such a relationship but they should also consider the situations mentioned above and it was also up to the Government to think about it.
Datuk Mohd Hishamudin Mohd Yunus, who led a three-judge panel, delivered the judgement after allowing an appeal by three transgenders who worked as (beauticians), setting aside a decision by the High Court in Seremban that rejected their judicial review application to challenge the Syariah law.
On Monday, the Negri Sembilan Mentri Besar Datuk Seri Mohamad Hasan said the state government would file an appeal to the Federal Court in the next few days.
Dr Mahathir also pointed that dressing was a contemporary issue.
"We say a certain clothing is men's clothing but men and women are also wearing jeans.
"Jeans is for men or women? This is a contemporary issue because in the past it was not a problem because men and women dressed differently but now things have changed," he said.