The formal opening ceremony for the Baltic Defence College took place on 24 February 1999. The first senior staff course at the College ran from August 1999 to June 2000 and the college's first thirty-two students all successfully graduated at an impressive ceremony on 22 June 2000. It was, however, a privilege for the thirty-seven students of the second senior staff course to witness the consecration of the College's Colours at a ceremony held at the Baltic Defence College on 23 October 2000.

Everyday, alongside the national flags of Estonia, Latvia and Lithuania, the College logo, which incorporates the national flags and a dark blue field to represent the aspirations of the three nations, flies in front of the college. The very logo was also used, during the first senior staff course, at the various national ceremonies where the College was present. The design of this logo has now been used as the basis for the design of the College Colours which also include the official badge of the College.

At a simple but moving ceremony, the new parade colours of the College were consecrated by the Chaplain of the Tartu Infantry Battalion of the Estonian Army. A short speech was made by the Defence Minister of Sweden who then hammered an engraved nail into the staff of the colours. Sweden is the lead nation for all the nations presently giving support to the Baltic Defence College project. A short speech was also made by the Defence Minister of Estonia who then hammered his engraved nail into the staff of the colours. Estonia is the host nation for the College. The ceremony was followed in Riga on 10. November by the Latvian Chief Chaplain and Latvian Ministry of Defence.

In the coming month similar ceremony will be held in Lithuania. In future the College Colours will be borne aloft by representatives of the College on the occasions when it is represented at the national ceremonies of Estonia, Latvia and Lithuania.