OBJECTIVES: Diagnosing epilepsy is a lengthy and burdensome process for patients and their family. Although the need for a more patient-centered approach in clinical practice is widely acknowledged, empirical evidence regarding patient preferences for diagnostic modalities in epilepsy is missing. The objectives of this study are 1) to identify to what extent important attributes of diagnostic procedures in epilepsy affect preferences for a procedure; 2) to determine the relative importance of these attributes; and 3) to calculate overall utility scores for routine electroencephalography (EEG) and magnetoencephalography (MEG) registrations. METHODS: A discrete choice experiment was performed to determine patients’ preferences, which involved presentation of pair-wise choice tasks regarding hypothetical scenarios. Scenarios varied along six attributes: “Way of measuring brain activity”; “Duration”; “Freedom of movement”; “Travel time”; “Type of additional examination”; and “Chance of additional examination”. Choice tasks were constructed using a statistically efficient design and the questionnaire contained 15 unique unlabeled choice tasks. Mixed multinomial logistic regression was used to estimate patients’ preferences. RESULTS: A total of 289 questionnaires were included in the analysis. McFadden’s pseudo R2 showed a model fit of 0.28 and all attributes were statistically significant. Heterogeneity in preferences was present for all attributes. “Freedom of movement” and “Chance of additional examination” were perceived as the most important attributes. Overall utility scores marginally differ between MEG and routine EEG. CONCLUSIONS: Our study suggests that the identified attributes are important in determining patients’ preference for epilepsy diagnostics. It can be concluded that MEG is not necessarily more patient-friendly than a routine EEG in primary diagnostics and, regarding additional diagnostics, patients have a strong preference for long-term 24h EEG over EEG after sleep deprivation. Furthermore, barring substantial heterogeneity within the parameters in mind, our study suggests that it is important to take individual preferences into account in clinical decision-making.