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The 7-methylguanosine cap structure at the 5' end of eukaryotic messenger RNAs is a critical determinant of their stability and translational efficiency (1-3). It is generally believed that 5'-end capping is a constitutive process that occurs during mRNA maturation and lacks the need for a quality-control mechanism to ensure its fidelity. We recently reported that the yeast Rail protein has pyrophosphohydrolase activity towards mRNAs lacking a 5'-end cap (4). Here we show that, in vitro as well as in yeast cells, Rail possesses a novel decapping endonuclease activity that can also remove the entire cap structure dinucleotide from an mRNA. This activity is targeted preferentially towards mRNAs with unmethylated caps in contrast to the canonical decapping enzyme, Dcp2, which targets mRNAs with a methylated cap. Capped but unmethylated mRNAs generated in yeast cells with a defect in the methyltransferase gene are more stable in a rail-gene-disrupted background. Moreover, railΔ yeast cells with wild-type capping enzymes show significant accumulation of mRNAs with 5' -end capping defects under nutritional stress conditions of glucose starvation or amino acid starvation. These findings provide evidence that 5' -end capping is not a constitutive process that necessarily always proceeds to completion and demonstrates that Rail has an essential role in clearing mRNAs with aberrant 5'-end caps. We propose that Rail is involved in an as yet uncharacterized quality control process that ensures mRNA 5' -end integrity by an aberrant-cap-mediated mRNA decay mechanism., The stability and translational efficiency of eukaryotic mRNAs are both influenced by the 5'-end cap (1-3). The cap is co-transcriptionally added and consists of a guanine nucleoside methylated at the [...]