Studies have highlighted the increasing fraction of unidentified organofluorine (UOF) compounds in human blood, whose health effects are not known. In this study, 130 whole blood samples from the Swedish general population were analyzed for extractable organofluorine (EOF) and selected per- and polyfluoroalkyl substances (PFAS). Organofluorine mass balance analysis revealed that 60% (0–99%) of the EOF in female samples could not be explained by the 63 monitored PFAS; in males, 41% (0–93%) of the EOF was of unidentified origin. Significant differences between both age groups and gender were seen, with the highest fraction of UOF in young females (70% UOF, aged 18–44), which is contrary to what has been reported in the literature for commonly monitored compounds (e.g., perfluorooctane sulfonic acid, PFOS). Increasing the number of monitored PFAS did not lead to a large decrease of the UOF fraction; the seven highest PFAS (C8–C11 PFCAs, C6–C8 PFSAs) accounted for 98% of sum 63 PFAS. The high fraction of UOF in human samples is of concern, as the chemical species of these organofluorine compounds remain unknown and thus their potential health risks cannot be assessed.