Background: According to data regarding number of physicians per 100 000 inhabitants, Croatia is below the European average. Under those circumstances, more attention needs to be devoted to Croatian medical schools and their applicants. Aims: This study sought to investigate admission trends of applicants to Croatian medical schools, analyse their demographics and motives for medical school enrollment. Methods: We collected admissions data of applicants to Croatian medical schools from 1979 to 2006. Motives for and against medical school enrollment were assessed in a survey of 1146 applicants (response rate 84%, 966/1146) and 98 final-year medical students (response rate 82%, 80/98) during July 2006. Results: The number of applicants to Croatian medical schools had been declining until 1995, it was lowest during the 1991-1995 war in Croatia and it has been rising from 1996 onwards. Majority of applicants in 2006/07 were women (69%). Most of the applicants attended general high schools. The applicants profess choosing a certain medical school for its quality and reputation, but we showed that they actually chose the closest school. The main motives for medical school enrollment were humanitarian and scientific, while main reasons against were perceived difficulty and financial burden. We showed that final-year medical students profess significantly lower interest in science and that they are less interested in altruistic aspects of medicine. Instead, great number of them would reconsider choosing medical studies again because of the corruption in medicine, fear of mistakes and uncertainty of employment. Conclusions: Following the admission trends in medical schools on a national level gives insight into the prospects of health care. Analysis of motives for and against medical school enrollment can provide guidelines for their improvement. Unless Croatia and other countries in transition devote more attention to recruitment, education and retention of physicians, the prospects of our healthcare are poor.