Cognitive deficits are often observed during the acute stage of encephalitis. It is presumed, that they persist and influence the long-term outcome, but data are very limited. Forty-seven patients with a definite or highly probable diagnosis of acute encephalitis were identified through retrospective analysis and prospectively followed up 6-84 months after the acute illness. P3 was carried out by oddball auditory paradigm, and P3 latency was measured as a marker of cognitive impairment. Healthy people, who matched the patients in age, were used as controls (n = 39). Statistical group analysis revealed no significant difference of the P3 latency between the patient and the control group. However a subgroup analysis showed significant longer P3 latencies in patients with a more unfavorable functional outcome at the time of follow-up. Patients with Herpes simplex virus (HSV) encephalitis had also more often abnormal P3 values compared to other etiologic subgroups, potentially indicating a higher percentage of patients with unfavorable cognitive outcome in this subgroup.