Objective: We evaluated the cerebrospinal fluid (CSF) cytokine profile and magnetic resonance imaging (MRI) findings in systemic lupus erythematosus (SLE) patients with central nervous system (CNS) involvement. Methods: Consecutive SLE patients followed at the rheumatology unit were enrolled into this study. Neurologically asymptomatic controls were matched for age and sex and recruited during myelography. SLE patients were assessed for disease activity (Systemic Lupus Erythematosus Disease Activity Index; SLEDAI) and cumulative damage (Systemic Lupus International Collaborating Clinics/American College of Rheumatology Damage Index; SDI). All subjects underwent MRI scans and blood and CSF withdrawal. Immunoglobulin G (IgG) and albumin were measured by nephelometry and link indexes were calculated according to the literature. Interleukin (IL)-12 p40/p70, interferon (IFN)-γ, tumor necrosis factor (TNF)-α, and IL-10 were measured by enzyme-linked immunosorbent assay. Results: We included 20 SLE patients (18 women, mean age 30.2 ± 9.2 years, range 19-45) with CNS manifestations. Increased IL-12 p40/p70, IFN-γ, TNF-α, and IL-10 CSF levels were observed in SLE patients. Mild pleocytosis was observed in 8 (66%) SLE patients and intrathecal production of IgG was observed in 2 (10%) SLE patients. Three (15%) SLE patients had demyelinating lesions, 5 (25%) patients had cerebral atrophy, and 12 (60%) patients had ischemic lesions on MRI. We observed that the cerebral lesion count was associated with CNS manifestations and SDI scores. We observed a significant cerebral volume reduction in SLE patients compared to controls (p < 0.001). Moreover, a direct correlation between cerebral volume reduction and CSF IFN-γ levels was observed (r = 0.5, p = 0.01). Conclusions: IL-12 p40/p70, IFN-γ, TNF-α, and IL-10 CSF levels were increased in SLE patients with CNS manifestations, but only IFN-γ was associated with a cerebral volume reduction in SLE, suggesting an immunological basis for global atrophy in SLE.