Up to 46% of patients with presumed autoimmune limbic encephalitis are seronegative for all currently known CNS antigens. We developed a cell-based assay (CBA) to screen for novel neural antibodies in serum and cerebrospinal fluid (CSF) using neurons and astrocytes derived from human induced pluripotent stem cells (hiPSC).In this study, hiPSC-derived neural cells seeded on 96-well plates (96-well CBA) were incubated with serum or CSF from 99 patients, including 42 with inflammatory neurological diseases (IND) and 57 with non-IND (NIND). The IND group included 11 patients with previously established neural antibodies, six with seronegative neuromyelitis optica spectrum disorder (NMOSD), 12 with suspected autoimmune encephalitis/paraneoplastic syndrome (AIE/PNS), and 13 with other IND (OIND). IgG bound to fixed CNS cells were detected using a combination of fluorescently-labelled antibodies. IgG-associated fluorescence intensity measures and microscopy observations were automated. IgG reactivity to neurons and astrocytes was further analyzed by flow cytometry. Peripheral blood mononuclear cells (PBMC) were used as CNS-irrelevant control target cells. Reactivity profile was defined as positive using a Robust regression and Outlier removal test with a false discovery rate at 10% following each individual readout.Using our 96-well CBA, we detected antibodies recognizing hiPSC-derived neural cells in 19/99 (19.2%) study patients. Antibodies bound specifically to astrocytes in nine cases, to neurons in eight cases and to both cell types in two cases. Microscopy single-cell analyses ascertained cellular distribution and binding specificity. Highlighting the significance of our novel 96-well CBA assay, the occurrence of CNS-specific antibody binding was more frequent in IND (15/42) than in NIND patients (4/57) (Fisher test,p=0.0005). Three of three patients with astrocyte-reactive (2 AQP4+ NMO, 1 GFAP astrocytopathy), and 3/4 with intracellular neuron-reactive antibodies (2 Hu+, 1 Ri+ AIE/PNS), as identified in validated diagnostic laboratories, were also positive with our CBA assay. Most interestingly, we showed antibody-reactivity in 2/6 seronegative NMOSD, 6/12 probable AIE/PNS, and 1/13 OIND. Flow cytometry using hiPSC-derived CNS cells or PBMC detected antibody binding in 13 versus 0 patients, respectively, establishing the specificity of the detected antibodies for neural tissue.Our unique hiPSC-based 96-well CBA allows for the screening of neuron-or astrocyte-reactive antibodies in patients with suspected immune-mediated neurological syndromes, and negative testing in established routine laboratories. Such a potent tool opens new perspectives in establishing early diagnosis of Ab-mediated diseases of the CNS.