In the period from 2001 to 2006, the Institute for strategic Studies under the President of Kazakhstan was headed M.S. Ashimbayev (appointed on May 18, 2000), currently First Deputy Chairman of the "Nur Otan" party, and B.K. Sultanov (appointed on July 7, 2005), currently Director of the Research Institute of International and Regional Cooperation of the Kazakh-German University.
The Institute strengthened its international cooperation. Thus, in 2001, a number of events and expert meetings with the delegations from China, Poland, Norway, India, Japan, France, and the UK were held and agreements on cooperation signed.
In 2001, the Institute acted as one of the main organizers for the presentation of the UNDP Human Development Report “Kazakhstan 2000 Fighting Poverty for a Better Future".
The cooperation the Institute established with the Organization for Security and Cooperation in Europe (OSCE) has proved to be the most fruitful.
In 2003, the KazISS marked the 10th anniversary. Within the anniversary events, the Institute established the tradition to hold Annual Almaty Conference on Security. The first forum was held on June 17-18, 2003, and covered the problems of regional security, political and economic development of the Central Asia in the context of Kazakhstan's interests. Special significant was a congratulatory letter from the President N.A. Nazarbayev of Kazakhstan.
The KazISS Annual Conference on security and regional cooperation has become an interactive platform to discuss and exchange the views on current issues by the experts from Central Asian countries. Since 2015, the conferences have been held in Astana.
In 2003. The KazISS marked its jubilee making the first issue of the English-language Central Asia's Affairs quarterly review. The first editorial board included A. Shomanov, G. Kurganbaeva, M. Laumulin, A. Nysanbaev, B. Sultanov, T. Umbetalieva. Since then, Maulen Ashimbayev has been chairing the editorial board of the journal.
Since 2004, the Institute launched the Kazakh-language "Khogham zhane Dauyr". The first editorial board included M. Tazhin, M. Ashimbayev, G. Korganbaev, M. Laumulin, A. Nysanbaev, and A. Shomanov.С 2004 г. начал выпускаться казахоязычное издание КИСИ «Қоғам және Дәуір». 
The second Annual Conference, held in June 2004, was on the regional cooperation of the Central Asian countries, the "Security and Regional Cooperation: Proceedings of the Second KazISS Annual Almaty Conference" were published consequently. The third Conference "China, Russia, the United States: Interests, Positions, Strategies and Interrelations in Contemporary Central Asia" was focused on the changes of the foreign policy courses of the three major actors and subsequent impact on Central Asia.
July 7, 2005, under the Decree of the President of Kazakhstan No. 561, Bulat Sultanov, a well-known expert, diplomat and Honored Worker of Kazakhstan, became the Director of the KazISS, heading the Institute for almost a decade from May 2005 to October 2014. Having extensive experience in international relations and diplomacy Dr. Sultanov initiated a number of international conferences and seminars on the issues related to the maintenance of security and stability in Central Asia and Kazakhstan. The close cooperation was established with European, primarily German partners, namely with the German Foreign Policy Society, Science and Policy Foundation, F. Ebert Foundation, J. Marshall Center as well as with Russian and Asian partners, for example those in China and India.
Thus, from 2001 to 2006, the Institute consolidated its international tires and fruitfully cooperated with a number of key research centers and foreign experts.
