Schistosomes are intravenous parasites\u00a0with ability to survive in the mammalian host for decades, using its blood as a source of nutrients.\u00a0The feeding process is multistep and takes place along the worm\u2019s alimentary tract, which comprises an (i) oral cavity opening to a short (ii) esophagus that is connected to the (iii) the gut caecum. The ultrastructureal morphology\u00a0of\u00a0Schistosoma mansoni\u00a0and\u00a0S. japonicum\u00a0has revealed the existence of two secretory cell masses surrounding the esophagus tube, referred to as the anterior and posterior esophageal glands (antESO and postESO, respectively). We recently established that the esophageal glands have a pivotal role in the first steps of blood processing. For instance, erythrocytes and leucocytes are quickly processed along the esophagus before they are propelled to the lower parts of the intestines for further digestion nutrient uptake. We propose that incorrect functioning of alimentary tract is associated with worms death by starvation. This was first observed in the self-cure response of Rhesus macaque (Macaca mulatta), one of few known vertebrate\u00a0hosts capable of combating the disease through worm elimination once the infection is stablished.\u00a0Classical immunoproteomics (2D-PAGE and Western blotting) has revealed potential targets in both exposed tegument and secreted gut proteins. Recently, a more detailed\u00a0investigation using S. japonicum\u00a0in the Rhesus model shed light on the possible operating mechanisms that prevent parasite feeding on blood. Ultrastructural studies and immunocytochemistry on surviving worms indicated the esophageal lumen and the gland secretions as the primary targets of a potent and protective humoral immune response that ultimately disrupts the esophageal functions. Therefore, the molecular characterisation of the esophageal gland constituents is imperative\u00a0if one intends to emulate the Rhesus self-cure response for therapeutic purposes. However, this is not a trivial task as\u00a0challenges are multiple. Perhaps, the most important caveat is that both anterior and posterior parts of the oesophageal gland represent a minor fraction of the whole parasite body (or even of its head), meaning that whole worm analyses are not sufficient for identification of genuine gland products. We tackled these challenges by developing a dissection technique on worms preserved in RNAlater solution aided by an essential set of scissors and tweezers that delivers adequate precision during the procedure. The method herein described is compatible with downstream Next Generation Sequencing. This methodology can be applied in the molecular characterisation of other schistosome organs and tissues that present a well-defined anatomic location.