The completion of projects for sequencing whole genomes such as those of human, Saccaromyces cerevisiae and Caenorhabditis elegans has led to a rapid increase in the availability of genetic information. The technology by which such information is acquired is having a major impact on the way we think about analysing the RNA and protein products of the gene transcription. Transcriptome analysis has, via microarray technology, managed to achieve a near genomic scale quantitative analysis of mRNA levels. Several other technologies such as quantitative reverse transcriptase polymerase chain reaction and representational differential analysis are also available for analysing gene products. Traditionally, protein analysis has been performed by assaying one particular protein at a time, with very little parallel analysis. As protein function is a direct consequence of the protein product of the gene and as mRNA levels do not always correlate well with protein, it is desirable to analyse the entire protein complement of a cell etc. on a similar scale to mRNA. Despite the clear interest in analysing the expression, structure and function of proteins at a genomic scale, they have proven less amenable to such generic, high-throughput approaches. This review highlights the current thinking in the area of proteome analysis and considers the potential for future technology development in the area of protein arrays.