White coffins were loaded into two Hercules transport aircraft near the Swiss town of Sion and landed at a military airport near Brussels from where undertakers collected them after a short ceremony. A third plane returned with their belongings.
In factories, offices and schools, Belgians stood silent. Buses, trams and some trains also stopped for passengers to pay their respects to the victims, most of them 11 and 12 year olds returning from a school skiing trip.
"The grief is so intense, but this helps," said one man from the town of Lommel - home to 17 of those killed - referring to acts of rememberance across Belgium.
Swiss police continued to investigate how the coach, carrying 52 passengers, crashed into a tunnel wall on Tuesday night, but one prosecutor cast doubt on reports in some Swiss and Belgian media that the driver had been busy loading a DVD player just before the crash.
Christian Varone, chief of police in the southern Swiss canton of Valais where the accident happened, said there were many possible explanations and police would take into account statements from the child passengers.
Factories fall silent
In Brussels, officials at the European Commission and NATO headquarters paused to remember the dead and in Ghent, workers at the Volvo car plant downed tools while cathedral and church bells rang out across the country.
On Thursday evening, the little church of St Joseph's in Lommel was swamped by 2,500 people who came to remember the 15 children and two school staff from the small town who had died.
The town plans a memorial ceremony on Wednesday, to be attended by members of the Belgian and Dutch royal families.
Flags were flown at half-mast on public buildings across Belgium, the Netherlands and the Swiss canton of Valais where the accident happened.
Six Dutch children were killed in the crash and four more were injured - Lommel is right by the Dutch border. Official British sources said one of the dead was an 11-year-old with joint Belgian-British nationality.
Of the survivors, six children with only light injuries returned to Belgium on Thursday. Six specialised medical planes were due to bring a further 14 more seriously injured children back on Friday and four more will stay in Swiss hospitals, three of them still in a critical condition.
Friday's national day of mourning is Belgium's first since 2004, which remembered 24 people killed in a gas explosion near the town of Ghislenghien.