Protein microarrays allow the simultaneous determination of a variety of parameters in parallel from minute amounts of sample, which allows for a high throughput analysis of translated gene functions. This article provides a wide and updated coverage of topics such as the complexity of this technology as compared to the gene expression technology, classification of protein microarrays, surface chemistry, detection methods, capture agents, experimental design, data analysis, standards, databases and interactions. The role of protein microarrays for the identification of cancer biomarkers in tissue and serum has also been elucidated. There are currently no guidelines on how to standardize these assays for biomarker discovery. Issues of sensitivity, specificity, difficulty in maintaining the native state of the protein upon surface immobilization, and limitations of the current arrays represent challenges that need to be overcome, and should be understood by those who are employing this parallel multiplexed technology in order to be able to achieve high throughput applications and minimize the occurrence of false positive and negative results.