Identification and isolation of differentially expressed genes is of great interest for a broad range of medical and biological research fields. For pharmaceutical and pharmacological applications the identification of target genes is of importance as well as the investigation of the transcriptional response to drug administration. Over the last two decades several techniques have been developed for analyzing gene expression in a variety of experimental contexts. Whereas microarrays represent closed architecture systems, restricted to well characterized models with a vast amount of available background data (e.g. human, mouse, etc.), open architecture systems allow detection of novel genes without a priori knowledge of the transcriptome. They are often based on amplification, subtraction and comparative display, and are well suited for so-called non-model organisms with little or no sequence data available. We review here the most common methods and their modifications: mRNA fingerprinting, differential display (DD), cDNA representational difference analysis (RDA) and suppression subtractive hybridization (SSH). The focus is on PCR-based methods that can be conducted with minimal bioinformatic and/or high throughput facility support, making them applicable in virtually any laboratory having access to basic molecular biology equipment. Furthermore we will give an insight into applications of these techniques in the pharmaceutical / pharmacological field.