Difficulty has been encountered when trying to identify ante mortem prognostic indicators for dogs with meningoencephalitis of unknown etiology (MUE). Identifying MRI imaging parameters associated with prognosis may impact treatment decision-making for clinician and owner. Our hypotheses for this retrospective cohort study are that dogs diagnosed with MUE that had midline shift on brain MRI would have a poorer survival compared to dogs without midline shift; and that younger age, lower weight, and low cerebrospinal fluid (CSF) cell count would be correlated with improved survival. Medical records were reviewed from two institutions. Inclusion criteria included: clinical signs referable to intracranial disease, brain MRI at presentation, abnormal CSF analysis, and negative infectious disease testing. Magnetic resonance imaging scans were evaluated for midline shift using the T2-weighted transverse image at the interthalamic adhesion and at the site of maximal deviation. Fifty-two dogs met the inclusion criteria. Median midline deviation was 0.12 cm. Median survival for dogs with no shift was 906 days and with shift was 84 days. Survival was not significantly different between groups (P = 0.11). This remained true when correcting for age (P = 0.22) and CSF TNCC (total nucleated cell count) (P = 0.12). Age at the time of diagnosis (P = 0.02) and CSF TNCC (P = 0.03) were significantly associated with survival. Cerebrospinal fluid protein value (P = 0.84) and weight (P = 0.82) were not significantly associated with survival. In this study of 52 dogs with MUE, MRI evidence of midline brain shift between 0.04 and 0.3 cm at the level of the interthalamic adhesion was not associated with shorter survival.