Quantification of gene expression is a crucial research tool in the life sciences, which makes it important to identify any factors that could compromise its accuracy. One of these factors are non‐polyadenylated (poly(A)−) transcripts, including circular RNAs (circRNAs) that can skew quantification of gene expression as they resemble messenger RNAs (mRNAs). Here, we highlight the impact circRNAs and other poly(A)− transcripts have on gene expression profiling and the biological conclusions drawn from such experiments. We also propose easily adoptable strategies to increase the accuracy of gene expression quantification.