Slovakia faces high youth unemployment rates while it also experienced large outflows of young post-accession migrants. This paper analyzes the impact of structural factors on propensity of youth to seek work abroad. The analysis merges macro-level labour market and economic performance indicators at the regional level with a unique micro-level dataset about migration intentions of graduating students collected in 2007. It evaluates relative importance of structural, labour market and individual factors in affecting migration choice of highly educated youth and finds that labour market conditions and indicators of structural change at the level of regions are significant predictors of propensity to migrate among the graduating students. The paper links these findings to massive and harsh adjustments that affected different Slovak regions disproportionately during the process of transition and contributed to mismatches between emerging job opportunities and qualifications of labour force, including the graduating youth.