The study is devoted to the transformation of the Slovak Academy of Sciences as a result of the social changes after November 1989. The transformation is traced in three stages. The first stage, which lasted from November 1989 to the election of a new leadership of the Academy in January 1990, was very dynamic. Strike committees were formed and there were changes in the leadership of the Academy and its institutes. The changes culminated in the election of a new democratically elected body: the Council of Scientists of the Slovak Academy of Sciences. The second stage occurred during the term of office of the new democratically elected leadership of the Slovak Academy of Sciences (1990 – May 1992). The coarsest deformations and injustices caused by the totalitarian regime were corrected, and the Academy developed a new character as a non-university academic institution. During the second leadership of the Academy (May 1992 – 1993), the transformation continued especially in the field of making scientific research more effective. The number of employees of the Academy was reduced by almost half, while scientific research was maintained on a good level. Apart from structural changes, the introduction of a grant system contributed to this. The transformation was largely completed in the period 1989-1993, and the Slovak Academy of Sciences was transformed into a democratically run, effective scientific institution, which carried out basic research and also in some areas targeted applied research.