The objective of our study is to assess differences in prevalence of multimorbidity by race/ethnicity. We applied the FP-growth algorithm on middle-aged and elderly cohorts stratified by race/ethnicity, age, and obesity level. We used 2016–2017 data from the Cerner HealthFacts electronic health record data warehouse. We identified disease combinations that are shared by all races/ethnicities, those shared by some, and those that are unique to one group for each age/obesity level. Our findings demonstrate that even after stratifying by age and obesity, there are differences in multimorbidity prevalence across races/ethnicities. There are multimorbidity combinations distinct to some racial groups—many of which are understudied. Some multimorbidities are shared by some but not all races/ethnicities. African Americans presented with the most distinct multimorbidities at an earlier age. The identification of prevalent multimorbidity combinations amongst subpopulations provides information specific to their unique clinical needs.