BioChips play a key role in the analysis of genes transcription or "expression profiling". The emergence of new chips that cover the entire genome of different organisms offers many opportunities to use for the comparison of expression levels of each gene depending on different parameters (cell type, cycle phase, etc.).
Thus, the activation or inhibition of many genes can be observed by comparing healthy cells versus diseased cells. Targeting these genes may lead to new therapeutic approaches.

Genotyping is also an important application of biochips which is to detect SNPs (Single Nucleotide Polymorphisms) as diagnostic "markers" of the potential onset of a particular disease.

Furthermore, CGH arrays (Comparative Genomic Hybridization) can detect variations in the number of DNA copies on the entire genome. This system is now widely used in cytogenetics for the determination of chromosomal diseases (Down syndrome, Turner syndrome, etc.) but also in oncology for the classification of tumors based on chromosomal rearrangements.