miRNA target genes prediction represents a crucial step in miRNAs functional characterization. In this context, the challenging issue remains predictions accuracy and recognition of false positive results. In this article myMIR, a web based system for increasing reliability of miRNAs predicted targets lists, is presented. myMIR implements an integrated pipeline for computing ranked miRNA::target lists and provides annotations for narrowing them down. The system relies on knowledge base data, suitably integrated in order to extend the functional characterization of targeted genes to miRNAs, by highlighting the search on over-represented annotation terms. Validation results show a dramatic reduction in the quantity of predictions and an increase in the sensitivity, when compared to other methods. This improves the predictions accuracy and allows the formulation of novel hypotheses on miRNAs functional involvement.