The Middle Eastern and North African (MENA) ethnic group is a diverse group composed of two primary subsets in the United States: Iranian and Arab Americans. We aimed to compare health risk factors, chronic health conditions, and mental health conditions of Iranian and Arab American adults in Northern California. We used cross-sectional electronic health record (EHR) data from a 2016 Northern California health plan study cohort to compare adults classified as Iranian or Arab American based on ethnicity, language, or surname. We produced age-standardized prevalence estimates of obesity, smoking, hyperlipidemia, prediabetes, diabetes, hypertension, depression, and anxiety for Iranian and Arab American men and women by age group (35-44, 45-64, and 65-84) and overall (35-84). We used generalized linear models to calculate prevalence ratios (PR) to compare Iranian and Arab American adults ages 35-84 on all health indicators. Compared to Arab Americans, Iranian Americans had a lower prevalence of obesity (PR: 0.77, 95% confidence interval, CI: 0.73, 0.82), current smoking (PR: 0.80, 95% CI: 0.73, 0.89), and ever smoking (PR: 0.95, 95% CI: 0.91, 0.99), but a higher prevalence of hyperlipidemia (PR: 1.09, 95% CI: 1.06, 1.12), prediabetes (PR: 1.12, 95% CI: 1.09, 1.16), depression (PR; 1.41, 95% CI: 1.30, 1.52), and anxiety (PR: 1.52, 95% CI: 1.42, 1.63). Similar patterns were observed for men and women. This work supports the need to collect granular data on race and ethnicity within the MENA ethnic group to improve identification in clinical care settings and population health reporting to better address the physical and mental health needs of different MENA subgroups.