Soluble endoglin (sEng) is a fragment of a membrane-associated receptor (CD105) expressed on endothelial cells, mesenchymal stem cells and trophoblast cells. It is considered as a regulatory factor involved in the development of preeclampsia (PE) and cancer-associated neo-angiogenesis. The purpose of this study was to describe a new sandwich ELISA for sEng quantification. In contrast to three commercial kits, the new ELISA was able to quantify sEng not only in blood plasma and cell culture supernatants, but also in urine and cerebrospinal fluid. The assay detected up to two orders of magnitude higher antigen levels than did the commercial kits. Using Western blot assay followed by SDS-PAGE or Blue Native PAGE, we demonstrated a heterogeneous nature of sEng molecules. Antigen heterogeneity is considered as a factor contributing to the pronounced differences in its content estimations by different ELISAs. We obtained evidence indicating that the assay was capable of detecting heterogenious sEng molecules. The new ELISA was validated as a quick, specific and accurate method for sEng quantification. Despite the differences in antigen content estimates, the assay had similar diagnostic performance as widely used commercial kit for the detection of severe PE in pregnant women based on plasma sEng contents. Moreover, the new assay was able to delineate diseased patients based on antigen levels in urine. Therefore, the new ELISA is a potentially valuable tool for in vitro and clinical studies.