AIM: To analyze a five-year publication output of the Zagreb University Medical School in scientific journals, especially in the journals covered by the Current Contents (CC), bibliographic database of the Institute for Scientific Information. METHODS: Medical School of the Zagreb University is organized in 10 preclinical, 6 public health, and 17 clinical departments, with 359 faculty members. Research activity is important for the academic promotion, with the number of publications (especially in journals covered by CC) and their impact as a key element. Bibliographic data on the published papers by the authors affiliated to the Zagreb University Medical School in the 1995-1999 period were searched in the CC and Biomedicina Croatica databases, according to the official faculty name list. The collected data were classified into three groups according to the source journals: papers published in international journals covered by the CC, Croatian journals covered by the CC, and Croatian journals not covered by the CC. The publication production was measured on individual and departmental levels by using two counting schemes: a) full publication to each author/department; and b) an equal fraction of a publication (1/n) to each author/department. RESULTS: In the 1995-1999 period, the faculty published 578 papers in the journals covered by the CC, 22.6% of them in the subset of Croatian journals. The differences among departments were considerable, with publishing activity per faculty member varying from 0.25 to 6.23 papers in CC journals and from 0.0 to 15.8 in Croatian non-CC journals. Preclinical departments published significantly less in the Croatian journals indexed in the CC then public health and clinical departments. There was a high variance in the number of publications on the individual level, with the 15.4% of the faculty in the professor rank and 45% in the assistant rank who did not publish a single paper in journals covered by the CC in the analyzed period. On the contrary, 10.1% of professors and 6.0% of assistants published more than 10 and more than 4 CC-indexed papers, respectively. A number of authors who have been very productive in international journals indexed in the CC (11 or more papers) did not publish in Croatian journals indexed in the same database, and vice versa. CONCLUSION: Publication output of the Zagreb University Medical School shows imbalances characteristic of a small scientific community: productivity with extreme values, relatively unsatisfactory number of papers published in the international journals covered by the CC database as compared to their importance in the process of the academic promotion, and disproportional role of certain domestic journals covered by the CC.