Before mRNAs are exported to the cytoplasm, it is crucial to check each mRNA for structural and functional integrity. Eukaryotic cells use several different mechanisms, collectively known as mRNA surveillance, to look for irregularities in mRNAs. Irregular or aberrant mRNA are rapidly degraded by various enzymes. If a defective mRNA escapes the surveillance, it would be translated into a protein which would either be non-functional or not function properly. One of the primary irregularities in mRNA is the presence of a premature stop codon. This is the result of sequence mutations that code for a Stop Codon prematurely in the reading frame. An estimated 30% of inherited genetic disorders in humans result from these mutations. These mRNAs are degraded in a pathway known as nonsense-mediated decay (NMD). NMD differs from other decay pathways by rapidly degrading mRNAs using 3′→5′ exonucleases.

Another prevalent decay mechanism detects lack of post-transcriptional modifications in mRNAs. RNA polymerase II transcripts are cotranscriptionally modified with a 5’ methylated G cap, and most of them have a chain of Adenine residues at the 3' end. Lack of either or both of these features, targets the mRNA for 5′→3′ exonucleolytic decay.

Other aberrations might be introduced if the mRNA has a single nucleotide mutation. Although this type of irregularity is most frequently observed in tRNAs, mRNAs can also be modified in the presence of reactive oxygen species (ROS), UV light, and alkylating agents. Chemical modifications caused by these agents are detected by NMD, non-stop decay (NSD) and no-go decay (NGD) pathways. All these pathways use specialized proteins that are sensitive to oxidative damage. These proteins recognize oxidized bases and direct the modified mRNAs to degradation pathways that use nucleases to digest the mRNAs.

While the degradation pathways discussed here target irregular mRNAs, they also down-regulate normal cellular mRNAs when they do not need to be translated. This process, formally classified as mRNA turnover, is also important to maintain optimum levels of mRNA in the cellular pool.