In order to determine the prevalence of neural autoantibodies in adult patients with drug-resistant temporal lobe epilepsy (DRTLE) of unknown etiology, we compared the characteristics of patients with and without autoantibodies and applied antibody predictive scores to the patients. Patients aged ≥18 years with DRTLE of unknown etiology and ≥12 months of evolution were prospectively recruited. Neural autoantibodies in serum and CSF were systematically determined in all patients. We created the ARTE (antibody in drug-resistant temporal lobe epilepsy) score based on the variables associated with the presence of neural autoantibodies. Twenty-seven patients were included. The mean (SD) age in years at the index date was 52 (±14.2) and at epilepsy onset was 32 (±17.1). The mean epilepsy duration was 19 (±12.5) years. Neural autoantibodies were detected in 51.85% (14/27) of patients. The presence of bitemporal, independent, interictal epileptiform discharges (BIIED) had a higher frequency in patients with neural autoantibodies (57.1% vs. 15.4%; p = 0.025) as well as those patients with a previous history of status epilepticus (49.2% vs. 0.0%; p = 0.007). The ARTE score showed an area under the curve (AUC) of 0.854. Using a cut-off point of ≥1, the sensitivity was 100% and the specificity was 46.1%, whereas when using a cut-off point of ≥3, the results were 35.7% and 100%, respectively. We found a high prevalence of neural autoantibodies in patients with DRTLE of unknown etiology, indicating an autoimmune mechanism. The presence of BIIED and a history of SE in DRTLE of unknown etiology are possible markers for autoimmune-associated epilepsy. The proposed ARTE score requires future validation in larger independent cohorts.