Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica surfaces.

While DNA microarrays are used to monitor gene expression, protein microarrays detect biologically relevant interactions of a fluorescently labeled protein with other proteins, DNA, or small molecules.

DNA microarray slides are often called gene chips or DNA chips. DNA chips are widely used to profile thousands of genes parallelly. Other than gene expression, they are also used in studying microRNA expression, DNA copy numbers, and single-nucleotide polymorphism detection. Commercially, these chips are used in biotechnology, forensics, toxicology, drug discovery, and targeted therapy for infectious and genetic diseases.

The chemically stable nature of DNA probes makes DNA chips the most popular of the microarray technologies. The covalently bound single-stranded DNA probe retains its native interactions despite harsh chemicals and temperatures that are used during probe loading and chip preparation.

The most obvious shortcoming of DNA microarrays is the prerequisite of a known target sequence. Because DNA microarray probes are designed to complement the target cDNA sequence, the sequence of the mRNA from which the cDNA is copied must be known. This makes the technology unusable while looking for novel mRNA sequences. For such purposes, RNASeq is the preferred albeit expensive option.