Arab Americans are a diverse ethnic group originating from a large geographic area in the Middle East and North Africa (MENA). We aim to characterize differences in health between Arab Americans from different geographic subgroups within MENA. We used cross-sectional electronic health record (EHR) data for a subset of 4913 Arab Americans aged 20-84 in a 2016 Northern California health plan study cohort who could be assigned to one of 4 geographic subgroups (Gulf, African, Levant, and Other) based on EHR ethnicity data. We calculated age-adjusted prevalence estimates for men and women and used generalized linear models to compare Gulf, African, and Other subgroups to Levant Arabs on risk factors (obesity and smoking), chronic conditions (diabetes, hypertension, hyperlipidemia, and asthma), and mental health (depression and anxiety). Among women, prevalence of smoking was lower among Gulf, African, and Other Arabs than Levant Arabs. Among men, prevalence of obesity, diabetes, and hyperlipidemia was lower among Gulf, African, and Other Arabs than Levant Arabs, while prevalence of depression was higher for these subgroups than Levant Arabs. We found substantial differences in health characteristics across Arab Americans from different geographic subgroups. Our results suggest that more detailed race and ethnicity information should be collected on Arab Americans to better understand their diverse health risks.