Tokom dva mandata koliko je Gligorov bio na mjestu predsjednika, u periodu 1991-1999, Makedonija je postala članica UN-a pod privremenom referencom "bivša Jugoslavenska Republika Makedonija", prihvatila Privremeni sporazum s Grčkom iz 1995. i prošla kroz kontroverznu ekonomsku tranziciju.
During Gligorov's two terms as president, between 1991 and 1999, Macedonia became a member of the UN under the temporary reference "the former Yugoslav Republic of Macedonia", accepted the 1995 Interim Accord with Greece and underwent a controversial economic transition.