While still being considered a neglected disease by the WHO, cystic echinococcosis represents a major public health and economic issue in many countries. Echinococcus granulosus, its causative agent, presents several interesting traits, and its developmental process shows a remarkable biological plasticity. In the past twenty years, several molecules from E. granulosus have been characterized; more recently, significant progress has been made with genomic, transcriptomic and proteomic analysis. In this review, we focus on progress made in the knowledge and understanding of the role played by important molecules involved in development, regulation of gene expression (homeobox genes and miRNAs), and fatty acid binding proteins. These proteins, given the restricted lipid metabolism of this parasite, could be key molecules in controlling this disease.