Secondary school began for boys on Saturday, without the participation of their female classmates.
Taliban issued a decree Friday directing boys to return to school, but not girls.
Taliban claimed they would like to establish a secure transportation system before girls can enter secondary school.
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On Saturday, Afghan girls did not return to secondary school after classrooms were reopened for first time since Kabul was overthrown by the Taliban.
Friday was Friday. The Taliban ordered boys to go back to school, but they left out girls.
A statement by the Taliban education ministry stated that "all male students and teachers should attend their educational institutions." This was for boys in grades 7-12.
On Saturday, a Taliban spokesperson stated that girls can still attend secondary school. A spokesperson for the Taliban told CNN that the Taliban wanted to first set up a "secure transport system" for its female students.
Zabiullah Mujahid, spokesperson for Taliban, stated that there are rules that must be followed during their classes so that they can be safe and sound.
Mujahid said that although there are still girls in universities who continue their education in both government-funded and private universities, we're currently working to give them the opportunity to continue in grade 6-12.
This decree marks the latest inflection in education and women's rights in Afghanistan. It was quickly overthrown by the Taliban last month, after the US announced that all troops had left the region.
The Taliban took over Afghanistan and renamed it the Islamic Emirate of Afghanistan. This is the same name as when the Taliban were in power between 1996 and 2001.
Women were subject to severe oppression under the Taliban regime. They were prevented from going to school or working. The militant group has vowed to respect women's rights within Islamic law. The Taliban's promise has been met with suspicion by Afghan women and human rights activists.
The Taliban stated earlier this month that women can study in universities provided they don't wear Islamic clothing and that classrooms are not segregated according to gender.
The edict to allow women higher education may be void if girls are denied the chance to go to secondary school in Afghanistan.