Most noncoding RNAs exert their function by interacting with other RNA molecules, as in the case of microRNA and their mRNA targets. Recent bioinformatical as well as experimental approaches produce thousands of novel RNA transcripts most of which cannot be annotated. Our best hope for elucidating the function of these novel transcripts is through identification of their interaction partners. In this talk I will review several approaches to predict the structure of two RNAs upon hybridization. I will present a fast method to compute the probability that some region of an RNA is unpaired and thus accessible for inter-molecular interactions (or, equivalently, the free energy needed to open up the site), as well as a method to quickly search for possible hybridization sites. The combination of these two approaches yields a promising approach to identify the RNA interaction partners of noncoding RNAs. The site accessibility is also a potent predictor of siRNA efficacy and can be used to improve microRNA target predictions.