During the meeting, Aliyev said Azerbaijan is interested in close cooperation with European institutions, the presidential website said.
McAllister, for his part, said the purpose of the European Parliament delegation's visit to Azerbaijan is to study the situation in the republic.
"The meeting addressed issues relating to cooperation between Azerbaijan and the European Union and their prospects, the current situation surrounding the settlement of the Armenian-Azerbaijani conflict over Nagorno-Karabakh, the protection of human rights, freedom of speech, etc.," the report said.
McAllister paid a visit to Azerbaijan on Monday as part of his tour of the countries of the South Caucasus. In Baku, the European Parliament delegation will also meet with the Azerbaijani parliamentary speaker, lawmakers and members of civil society organizations.