BACKGROUND: One of the most frequently used parameters for evaluating scientific publications is that of impact factor (IF) published in the Science Citation Index-Journal Citation Reports (SCI-JCR) which evaluates the number of citations a journal receives on behalf of other journals. The present study analyzed the Spanish biomedical journals included in the SCI-JCR by the IF. METHODS: The IF were obtained from the SCI-JCR (198-89). The journals were evaluated by the IF and the weighed impact factor (WIF) calculated according to WIF = (IF/MIF) X 100 in which MIF = maximum IF of the considered area. RESULTS: Nine Spanish biomedical journals were included in the SCI-JCR, four being basic sciences (Histology and Histopathology, Inmunologia, Methods and Findings in Experimental and Clinical Pharmacology, Revista Espanola de Fisiologia) and five clinical journals (Allergologia et Immunopathologia, Medicina Clinica, Nefrologia, Revista Espanola de las Enfermedades del Aparato Digestivo, Revista Clinica Espanola). Their IF were much lower than the most important journals in each area with the mean (+/- standard deviation) being 0.21 +/- 0.22 (range 0.016-0.627). The mean WIF was 2.88 +/- 4.07 (0.16-12.82). The journals of basic sciences had higher IF and WIF than the clinical journals (p < 0.05). Only the four journals of basic sciences were included in the SCI. Four journals, those of basic sciences, are preferentially or exclusively published in English and other five are published in Spanish. The differences in IF among these groups were not significant (p = 0.06) while those of WIF were significant (p < 0.05). The number of Spanish biomedical journals in the SCI-JCR has risen from 1 in 1980 to 9 in 1989 with IF which have evoluted variably. CONCLUSIONS: In mind of impact factor, the contribution of Spanish journals is low, with that of biomedical sciences being higher than that of clinical journals. Language and inclusion in the Science Citation Index may explain, at least in part, the low impact factors obtained.