MicroRNAs are short (20-22) nucleotide non-coding RNAs involved in post-transcriptional regulation of gene expression. One of the essential requirements to understand the function of a microRNA is to know the genes it regulates, the so-called targets of the microRNA. It is believed that in plants most target sites present a near perfect complementarity to the sequence of the microRNA. However, in animals most target sites present lower number of complementary nucleotides. It is therefore difficult to design target prediction methods that simultaneously have high specificity and sensitivity. It has recently been discovered that in animals microRNAs not only suppress translation but also induce the destabilization of mRNA transcripts. This discovery has opened up the possibility of using data from microarray assays, performed on cells where microRNA expression is modified, to predict its targets. In the first part of the talk we will review current sequence-based microRNA target prediction tools. In the second part of the talk we will show how microarray data can be used to improve microRNA target prediction.