Seven thousand people have been evacuated from their homes in a coordinated population swap agreed between the Syrian government and the opposition.
Some 5,000 people were evacuated from two pro-government areas near Aleppo, a rebel stronghold that forces loyal to President Bashar al Assad have been trying to recapture.
And some 2,350 opposition fighters have been moved from two opposition-held areas near the capital, Damascus.
The evacuations form part of a deal to evacuate some 30,000 Syrians from pro-government and pro-rebel besieged areas over the next two months.
Some have criticised the deal as forced displacement, while others fear they are being gathered for a final government offensive to defeat them.
Many medical workers, activists and former fighters have refused to redeploy with the military that once shelled their homes.
Some families have been split up in the move.
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Evacuee Muhammad Darwish said: "Honestly, when we left Madaya, I felt sadness, anger and sorrow. But now, on the road, I don't feel anything. I feel cold as ice."
The 19-year-old, who left his parents behind in Madaya, went on: "There was no heating, no food, nothing to sustain our lives. We left so that God willing (the siege) may ease on those who remain."
The evacuation deal was brokered by Qatar, negotiating on behalf of the rebels, and Iran, on behalf of the government, in March.
The United Nations is not supervising the evacuations.
Mr Assad has spoken out for the first time since a chemical attack in Idlib province on 4 April widely blamed on his forces.
About 80 people, including many children, are believed to have died in the attack.
Mr Assad said the attack is a "100% fabrication" , insisted he gave "no order to make any attack" and claimed "even if we had (chemical weapons) we wouldn't use them."