Background Both C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) can be elevated in systemic lupus erythematosus (SLE) flare and infection, and are therefore of limited utility for distinguishing between the two conditions in febrile SLE patients. Methods: A medical records review of hospitalizations (1997-2006) of SLE patients in the Michigan Lupus Cohort was performed. Eligible hospitalizations were those in which patients presented with a temperature of >100.3 degrees For with subjective fevers as a presenting complaint at admission. Detailed demographic, clinical, and laboratory data were collected. Multivariable logistic regression was used to examine the associations between ESR and CRP and the outcome of flare vs infection, adjusted for confounders. Results: Among 557 SLE patients screened, there were 53 eligible hospitalizations (28 flares and 25 infections). Each unit increase in the ratio of ESR:CRP was associated with a 17% increase in the odds of fever being attributable to SLE flare compared to infection (OR 1.17, 95% CI 1.04, 1.31; p = 0.009), when adjusted for white blood cell count, SLE duration, sex, race, and age. ESR and CRP were not individually associated with flare vs infection when modeled with their ratio. Conclusions: The ratio of ESR:CRP may provide diagnostic value beyond individual ESR and CRP levels in distinguishing flare vs infection in SLE patients presenting with fever.