OBJECTIVES: During 1991-2000, Japan contribution to the top basic and clinical science journals was less than 1% and 3%, respectively. The objective of this study was to compare the Japanese representation in 7 major general medicine journals and 6 basic science journals between the years 1991-2000 and 2001-2010. METHODS: Retrospective observational study. We measured the frequency of journal article publications in PubMed from Japan in both seven high-impact general medical and internal medicine journals and six high-impact basic science journals using Boolean operators to connect name of the journal, year of publication and corresponding authors’ affiliation with different universities, cities and places in Japan. RESULTS: Japan represented 0.66% (260/39,255) and 0.74% (265/36,038) of journal articles in 7 of the top general medicine journals during 1991-2000 and 2001-2010, respectively. In contrast, the respective representation in 6 of the top basic science journals was 2.51% (849/33,779) and 3.60% (1364/37,908), respectively. Overall, we observed that the proportion of Japan-originated articles published in the top general medicine journals during 2001-2010 remained unchanged compared to 1991-2000 (P=0.255). However, the Japanese representation in basic science journals during 2001-2010 increased significantly compared to 1991-2000 (P<0.001). Japanese representation in basic science journals had an upward trend during the 1991-2000 period (P<0.001) but remained flat during 2001-2010 (P=0.177). In contrast, the trend of Japanese representation in general medicine journals remained flat during the period of 1991-2000 (P=0.273) but exhibited a marginally downward trend during 2001-2010 (P=0.073). CONCLUSIONS: Overall, the Japanese representation in top general medicine journals has remained negligible and unchanged over the last two decades. Representation in basic science journals remained unchanged during the time period of 2001-2010, although it had shown an upward trend during the years 1991-2000. Interventional measures are needed to address these trends.