RNAhybrid is an online tool for predicting microRNA (miRNA) target sites. It offers a flexible, fast, and efficient method for identifying potential miRNA target interactions. The tool allows users to input their own miRNA and target sequences and provides various options to control the type of interaction being analyzed. RNAhybrid can be used as a web service, enabling remote calls from user-implemented programs, eliminating the need for local installation. Recent updates include the ability to disallow G:U base pairs in the seed region and a seed-match speed-up, which accelerates the program by a factor of 8. RNAhybrid has been used over 1000 times per month and has demonstrated high specificity in predicting targets in Drosophila melanogaster. It has also been used to predict a non-canonical target site for miR-241 in the 3'-untranslated region of lin-39 in Caenorhabditis elegans. RNAhybrid is available at http://bibiserv.techfak.uni-bielefeld.de/rnahybrid. It is one of the few online tools available for miRNA target prediction, alongside Diana microT and miRU. RNAhybrid's flexibility is demonstrated by its ability to handle various types of target interactions, including those that do not follow the traditional seed match rules. The tool has been used to analyze potential non-canonical target sites for miRNAs in C. elegans, showing the importance of 3'-complementarity in target specificity. RNAhybrid is a valuable resource for researchers studying miRNA target interactions.RNAhybrid is an online tool for predicting microRNA (miRNA) target sites. It offers a flexible, fast, and efficient method for identifying potential miRNA target interactions. The tool allows users to input their own miRNA and target sequences and provides various options to control the type of interaction being analyzed. RNAhybrid can be used as a web service, enabling remote calls from user-implemented programs, eliminating the need for local installation. Recent updates include the ability to disallow G:U base pairs in the seed region and a seed-match speed-up, which accelerates the program by a factor of 8. RNAhybrid has been used over 1000 times per month and has demonstrated high specificity in predicting targets in Drosophila melanogaster. It has also been used to predict a non-canonical target site for miR-241 in the 3'-untranslated region of lin-39 in Caenorhabditis elegans. RNAhybrid is available at http://bibiserv.techfak.uni-bielefeld.de/rnahybrid. It is one of the few online tools available for miRNA target prediction, alongside Diana microT and miRU. RNAhybrid's flexibility is demonstrated by its ability to handle various types of target interactions, including those that do not follow the traditional seed match rules. The tool has been used to analyze potential non-canonical target sites for miRNAs in C. elegans, showing the importance of 3'-complementarity in target specificity. RNAhybrid is a valuable resource for researchers studying miRNA target interactions.