Lupus nephritis (LN) carries high morbidity and mortality and whenever added to neuropsychiatric manifestations lead to more unfavorable prognosis. Though silent brain MRI findings in systemic lupus erythematosus (SLE) had been widely studied, the current work focused on LN patients comparing them to those without kidney affection, studying their cerebral MRI and its correlation with the histopathological classes of LN and disease activity. This may enable us to know more about early brain affection in LN patients for better follow up, management, and prognosis of this serious comorbidity. Cerebral MRI and MRA were studied in 40 SLE patients without neuropsychiatric manifestations; 20 LN patients with different histopathological classes and 20 patients without kidney affection. Disease activity was assessed for all patients using SLE disease activity index (SLEDAI). Abnormal MRI brain findings were more common in LN patients “though non significant” (P = 0.9). The most common lesions were white matter hyperintense lesions (WMHLs). Number and size of such lesions were significantly higher in LN patients (1.8 fold that of non nephritis, P = 0.003 and 0.03, respectively) and positively correlated with urea, creatinine, urinary albumin/creatinine ratio, SLEDAI, ESR, CRP, and grades of renal biopsy and negatively correlated with C3 and C4. Cortical atrophy and prepontine space dilatation were also significantly higher in LN patients (P = 0.01). Asymptomatic MRI brain lesions whenever present in LN patients, they are usually clinically significant and well correlate to laboratory parameters of LN, grades of renal biopsy, and disease activity independent to age, sex and hypertension.