A judicial source on Friday said the trials will start after the current Muslim festival of Eid al-Adha.
The al-Qaida suspects include two extradited by Saudi Arabia and one by Kuwait last year, the source said.
The suspects "have links with those accused of bombing the French supertanker Limburg in October 2002 and with other terrorist attacks which took place in Yemen over the past two years".
The 800 other suspects who will be tried in batches are members of the Faithful Youth organisation which was headed by a Yemeni rebel preacher killed by the army last September.
The Yemeni government announced last September that the army had killed Shaikh Husain Badr al-Din al-Huthi, nearly three months after he started a rebellion in the country's mountainous northwest, triggering clashes which left more than 400 people dead.
Yemen, which has cracked down on suspected al-Qaida members, has already tried and convicted several people over the Limburg attacks and the 2000 bombing of the US navy destroyer Cole in an Aden port. Seventeen US sailors died in the attack.
The appeals court will deliver its verdict in the Limburg case on 5 February and in the Cole case on 26 February.