AIM: To investigate fellowship outcomes among junior researchers in medicine, supported by the Ministry of Science, Education, and Sports of the Republic of Croatia. ----- METHODS: We used the data on junior researchers whose fellowships terminated between 1999 and 2005. Employment outcomes and scientific productivity, measured by the number of published articles indexed in the Web of Science database, were analyzed for every junior researcher. The data were analyzed using chi2 test, Mann-Whitney test, Kruskal-Wallis test, Breslow test, and logistic regression. ----- RESULTS: Only 12% of junior researchers obtained a degree of Doctor of Philosophy (PhD) during fellowship. At the same time, 55% of junior researchers with a Medical Doctor degree terminated the fellowship and got employed in the health system during the same month. Terminating and re-employing in same month was most common among junior researchers who got employed by clinics and hospitals (odds ratio, 7.78; 95% confidence interval, 2.22-27.24). Also, it was less common among female than male junior researchers (odds ratio, 0.50; 95% confidence interval, 0.28-0.90). ----- CONCLUSION: This study suggests that junior researchers in medicine commonly used their fellowship as a short-term employment option. The direct consequence of this is the low percentage of obtained PhD degrees during the fellowship period. Additionally, this article provides an insight into the current status and future of the fellowship programs in medicine, with special emphasis placed on the potential changes that might occur as a consequence of physician shortage in Croatia.