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Background Cognitive event-related potentials (ERPs) have been previously correlated with T2 lesion load (Τ2LL) in patients with multiple sclerosis (MS). It is currently unknown, however, whether ERPs also correlate with brain atrophy or the presence of T1 hypointense lesions (“black holes”) which reflect tissue destruction and axonal loss. The primary aim of the current study is to explore the effect of neuroradiological parameters such as brain atrophy, T1 and T2 lesion load on auditory ERPs in MS patients. In addition, we correlated cognitive impairment with neurophysiological (ERP) and neuroradiological (MRI) variables and investigated whether a combination of ERP and MRI parameters is capable of distinguishing patients suffering from secondary progressive (SP), primary progressive (PP) and relapsing-remitting (RR) MS. Materials and methods The study sample consisted of fifty nine MS patients (mean age±SD: 37.82±1.38 years; average disease duration: 6.76±5.3 years) and twenty six age-matched controls (mean age±SD: 41.42±15.39 years). The patients’ EDSS and NRS scores were 3.77±2.14 (range: 1–7.5) and 75.88±11.99 (range: 42–94) respectively. ERPs were recorded using the auditory “odd-ball” paradigm. T1 and T2 lesions were automatically segmented using an edge-finding tool and total lesion volumes were calculated. MRI measures of brain atrophy included third ventricle width (THIRDVW) and the ratio of mid-sagittal corpus callosum area to the mid-sagittal intracranial skull surface area (CC/MISS). Statistical analysis was performed using multiple regression, principal component (PCA) and discriminant analysis. Results T1 lesion load emerged as the most significant predictor of P300 and N200 latency. The rest of the endogenous ERPs parameters (P300 amplitude, N200 amplitude) were not significantly correlated with the MRI variables. PCA of pooled neuroradiological and neurophysiological markers suggested that four components accounted for 64.6% of the total variability. Discriminant analysis based on ERP & MRI markers classified correctly 79.63% of patients in RR, PP and SP subgroups. Conclusion T1 lesion load is the most significant MRI correlate of auditory ERPs in MS patients. Importantly, ERPs in combination with MRI variables can be usefully employed for distinguishing patients with different subtypes of MS.