Increasingly large numbers of microRNAs are being discovered everyday and their role in gene regulation being better understood. A number of computational methods for the prediction of microRNAs are homology based and can miss out on any unique microRNA. A part of this work was dedicated to the development of an effective ab initio pipeline (CIDmiRNA) for microRNA prediction. This pipeline showed a sensitivity of 91.7% for Human microRNA prediction. Entamoeba histolytica is the causative agent of human invasive amoebiasis, a common health problem in developing countries. Despite a lot of available information about the biology of this organism, no microRNAs have yet been reported. In this work, 6 putative microRNA genes were discovered in E. histolytica using CIDmiRNA, a computational prediction pipeline. Also, the intergenic regions of E. histolytica were analysed, exploring for novel genes using computational methods. We were able to predict at least 2 highly likely candidates for being novel genes missed out in the current annotation.