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Systemic lupus erythematosus (SLE) is a rheumatic disease, which during its evolution may present neurocognitive dysfunction with fronto-subcortical compromise. However, there is no enough published evidence regarding the relationship between cognitive dysfunction and SLE activity and SLE induced damage. The objective of the study was to analyze this association. We designed an observational cross-sectional study including 84 patients with SLE. We used the SLEDAI index to evaluate activity and the SLICC index to evaluate cumulative damage. We used neuropsychological tests to assess the presence of cognitive symptoms, global cognitive function, verbal and visual memory, visual-construction, semantic verbal fluency, processing speed and working memory. Scores more than 1.5 standard deviations below adjusted normal values were considered as cognitive dysfunction. We observed a statistically significant association between the higher value of SLEDAI and working memory impairment and a higher value of SLICC and viso-construction and semantic verbal fluency impairment. The association observed in SLE patients between disease activity or damage and some cognitive domains may be involving different pathophysiological brain mechanisms of different areas with different degrees of severity and vulnerability.