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Background  African Americans with systemic lupus erythematosus (SLE) have increased renal disease compared to Caucasians, but differences in other comorbidities have not been well-described. We used an electronic health record (EHR) technique to test for differences in comorbidities in African Americans compared to Caucasians with SLE.    Methods  We used a de-identified EHR with 2.8 million subjects to identify SLE cases using a validated algorithm. We performed phenome-wide association studies (PheWAS) comparing African American to Caucasian SLE cases and African American SLE cases to matched non-SLE controls. Controls were age, sex, and race matched to SLE cases. For multiple testing, a false discovery rate (FDR)  p  value of 0.05 was used.    Results  We identified 270 African Americans and 715 Caucasians with SLE and 1425 matched African American controls. Compared to Caucasians with SLE adjusting for age and sex, African Americans with SLE had more comorbidities in every organ system. The most striking included hypertension odds ratio (OR) = 4.25, FDR  p  = 5.49 × 10 − 15 ; renal dialysis OR = 10.90, FDR  p  = 8.75 × 10 − 14 ; and pneumonia OR = 3.57, FDR  p  = 2.32 × 10 − 8 . Compared to the African American matched controls without SLE, African Americans with SLE were more likely to have comorbidities in every organ system. The most significant codes were renal and cardiac, and included renal failure (OR = 9.55, FDR  p  = 2.26 × 10 − 40 ) and hypertensive heart and renal disease (OR = 8.08, FDR  p  = 1.78 × 10 − 22 ). Adjusting for race, age, and sex in a model including both African American and Caucasian SLE cases and controls, SLE was independently associated with renal, cardiovascular, and infectious diseases (all  p  < 0.01).    Conclusions  African Americans with SLE have an increased comorbidity burden compared to Caucasians with SLE and matched controls. This increase in comorbidities in African Americans with SLE highlights the need to monitor for cardiovascular and infectious complications.    Electronic supplementary material  The online version of this article (10.1186/s13075-018-1561-8) contains supplementary material, which is available to authorized users.

Phenome-wide association study identifies marked increased in burden of comorbidities in African Americans with systemic lupus erythematosus