Morpholino technology has been widely used by developmental biologists for over a decade. However, in recent years numerous authors have expressed concerns about the usefulness of morpholinos and their worrisome side effects and discrepancies between phenotypes produced by morpholinos and those resulting from mutation(s) in the gene of interest. Such excellent and extremely informative studies looked at various potential explanations and remedies but they have not discussed the possibility that some of the off-target effects and discrepancies present in morpholino knockouts may result from the unintended interference with mRNA structure and function. Here, to supplement the ongoing worldwide discussion on the subject, we present another potential explanation for such unexpected effects of morpholino technology.