One of the major challenges governments after the breakdown of communism in Central and Eastern Europe faced was a necessity to adjust judiciaries to new conditions. This comparative case-study aims to qualitatively analyze different paths in reforming judiciaries taken by the Czech Republic and Slovakia prior to their EU accession as well as their subsequent developments. Research shows that Slovakia in an attempt to prove itself as a trustworthy candidate for EU integration took a more radical approach to establishment of judiciary independence than its Czech counterpart which rather relied on a gradual transfer of competences to judicial self-administration. Consequently, Slovakia needed to mitigate unintended consequences with a series of amendments resulting in a chaotic legislative setup, while the Czechs proceeded with fewer and better reasoned interventions in the design of institutions of judicial independence and accountability.