Background: Early and accurate diagnosis is crucial for effective prevention and treatment of severe mental illnesses, such as schizophrenia and bipolar disorder. However, identifying these conditions in their early stages remains a significant challenge. Our goal was to develop a method capable of detecting latent disease liability in healthy volunteers. Methods: Using questionnaires examining affective temperament and schizotypal traits among voluntary, healthy university students (N = 710), we created three groups. These were a group characterized by an emphasis on positive schizotypal traits (N = 20), a group showing cyclothymic temperament traits (N = 17), and a control group showing no susceptibility in either direction (N = 21). We performed a resting-state EEG examination as part of a complex psychological, electrophysiological, psychophysiological, and laboratory battery, and we developed feature-selection machine-learning methods to differentiate the low-risk groups. Results: Both low-risk groups could be reliably (with 90% accuracy) separated from the control group. Conclusions: Models applied to the data allowed us to differentiate between healthy university students with latent schizotypal or bipolar tendencies. Our research may improve the sensitivity and specificity of risk-state identification, leading to more effective and safer secondary prevention strategies for individuals in the prodromal phases of these disorders.