GPI anchors many proteins to the cell surface. GPI precursor has three mannoses, all of which are modified by ethanolamine-phosphate (EthN-P). It has been believed that EthN-P on the third mannose is always used as a bridge to the protein and EthN-P on the second mannose is removed after GPI is attached to the protein. Based on the finding that PIGB-knockout cells lacking the third mannose and PIGO-knockout cells lacking EthN-P linked to the third mannose expressed low levels of CD59 and DAF, GPI-APs and that those residual GPI-APs were lost by further knockout of PIGG. Using mass-spectrometry we determined that CD59 expressed on PIGB-knockout cells is attached to GPI via EthN-P linked to the second mannose. This linkage structure is also found in wild type cells. Our data modifies the current view of GPI anchors and provides mechanistic basis of inherited GPI deficiency caused by PIGG mutations.