OBJECTIVES: Data from Sweden (Nyren 1992) shows the annual frequency of consultations for functional dyspepsia (FD) to be estimated at 47/1000 population with a costs estimated at $US113,630/1000 population (1991 dollars). No published data exists for US based employers on the costs associated with FD. To assess the economic burden of FD associated with medical costs and work loss from an employer perspective. METHODS: A review was conducted using a person-centric database containing costs from multiple large geographically diverse US based employers between 2001-2004. Claims data included pharmacy, medical, short- and long-term disability (STD, LTD), sick leave (SL), and productivity measurements. Comparisons were made between FD employees (ICD-9 code of 536.8) and employees without FD. Data were compared for a 12-month period beginning 3 months prior to the first diagnosis of FD (the index date). The average index date from the FD cohort was assigned for the control group. Multiple regression and Markov modeling techniques along with Charlson Co-Morbidity Index to adjust for variances. RESULTS: Data were available for 1,669 employees with FD and a control group of (274,206) employees without FD. The FD group's costs (per employee/year) were twice as high ($3,676) summed across all direct medical and work absence measures (P<0.0001). The individual differences (favoring FD) in medical and pharmacy costs were $3420 and $365, respectively (both P <0.0001). Work absence costs had differences of $103 (SL, P <0.0001), $104 (STD, P = 0.0370), $7 (LTD, P = 0.6551). Measured units of productivity were 2 units less/hour with the FD group (P=0.055). CONCLUSION: This study confirms earlier work from Sweden, but shows that in the US, FD can be costly to employers. Physicians and patients need more education on the ROME II criteria and how to integrate this information into improving medical and pharmaceutical costs.