Summary The goal of the current investigation was to develop a systematic method to validate the accuracy of an automated method of sleep spindle detection that takes into consideration individual differences in spindle amplitude. The benchmarking approach used here could be employed more generally to validate automated spindle scoring from other detection algorithms. In a sample of Stage 2 sleep from 10 healthy young subjects, spindles were identified both manually and automatically. The minimum amplitude threshold used by theprana® (PhiTools, Strasbourg, France) software spindle detection algorithm to identify a spindle was subject-specific and determined based upon each subject’s mean peak spindle amplitude. Overall sensitivity and specificity values were 98.96 and 88.49%, respectively, when compared to manual scoring. Selecting individual amplitude thresholds for spindle detection based on systematic benchmarking data may validate automated spindle detection methods and improve reproducibility of experimental results. Given that interindividual differences are accounted for, we feel that automatic spindle detection provides an accurate and efficient alternative approach for detecting sleep spindles.