The new EU-Russia agreement is set to replace the 1997 Partnership and Cooperation Agreement, which was extended for a year when it expired in December 2007.
Russia's envoy to the European Union, Vladimir Chizhov, who also heads the Russian delegation at the talks, said he did not expect the talks to be easy.
"Although I am setting off for the talks in a good state of mind, I do not expect them to be either easy or swift," he said. "However, the very fact that they have been resumed gives cause for optimism."
On September 1, the EU announced that it had suspended talks on the pact with Russia due to the presence of Russian troops in Georgia more than two weeks after the end of a brief war with the South Caucasus state over breakaway South Ossetia. The EU said it would not resume the talks until Russia pulled all its troops in Georgia back to their pre-conflict positions.
Russian troops completed a pullout from buffer zones in Georgia in October, although questions still remain over the amount of soldiers stationed in South Ossetia and Abkhazia, another disputed Georgian republic. Russia recognized both republics as independent states at the end of August.
The resumption of talks was agreed on November 14, during the Russia-EU summit in Nice. All but one of the EU's 27 members supported the decision.
Lithuania made it clear that it would continue to oppose a resumption of negotiations with Russia. However, the negotiations do not require the support of all 27 member states. Poland had also opposed negotiations on the new Russia-EU agreement, set to cover political, economic and trade relations, but lifted its objections before the Nice talks.
The earlier first round of talks on the new deal was delayed due to Polish and Lithuanian opposition.