The students had travelled to Iguala to protest against what they believed were unfair hiring practices and to raise money for their college. They were all training to be teachers.
As part of the protest, they planned to disrupt a speech made by the Mayor of Iguala's wife, Maria de los Angeles Pineda.
But police opened fire on the students' bus, killing three on the bus and another three in vehicles close by.
Forty-three students attempted to flee before being apprehended by police.
A local gangster has said the police turned these students over to a local drugs gang and that they haven't been seen since.
Vatican Radio claims the students were burnt alive by the criminal gang.
The Pope said: "I would like to raise a prayer and draw close in our hearts to the people of Mexico, who are suffering from the loss of these students and many similar problems.
"May our hearts be close to them, in prayer at this time."
The Mexican attorney general has accused the Mayor of Iguala, Jose Luis Abarca, of ordering the police to stop the students' disruption of his wife's speech.
On the day of the attacks, Mr Abarca and Mrs Pineda took a leave of absence. They haven't been seen since and are now considered fugitives by the Mexican state.