Recently proteome analysis has rapidly developed in the post-genome era and is now widely accepted as a complementary technology to genetic profiling. The improvement in the technology of both two-dimensional electrophoresis (2-DE) analysis as well as protein identification has made proteomics a valuable and powerful tool to study human diseases. A combination of conventional proteome analysis with serology has been developed as a promising experimental approach for the discovery of serological markers in different malignancies. However, the design of proteome-based studies has to be carefully performed since there are a number of critical needs for systematic and reproducible proteome analysis. In particular, the selection of tissue and its preparation represent an important step in proteome analysis. Besides the preparation of protein samples, the 2-DE and protein identification is a further critical issue. So far proteome-based technologies have been successfully used in tumor immunnology for the identification of tumor-specific autoantigens. Similarly, this technology has been employed for the detection of virulence factors, antigens and vaccine candidates in infectious diseases, as well as for the identification of diagnostic and prognostic markers, suggesting that proteome-based analysis is a promising tool for the identification of prognostic, diagnostic markers as well as for novel therapeutic targets which could be used for treatment of diseases. The integration of proteome-based approaches with data from genomic or genetic profiling will lead to a better understanding of different diseases, which will then contribute to the direct translation of the research findings into clinical practice.