OBJECTIVES: The etiology of functional dyspepsia (FD) is debated. However, limited published data exist on the associated co-morbid conditions with FD. This study aimed to assess the odds (likelihood) of having FD based on the presence of other objectively defined comorbid conditions. METHODS: Retrospective database analysis on a 4-year study period (2001-2004), using payroll data and adjudicated health insurance medical and prescription claims on more than 300,000 employees. Study comparisons were performed among employees with FD (ICD9= 536.8x) and propensity-score-matched employees without FD (controls, matched on age, gender, tenure with employer, marital status, race, region, salary, exempt status, and full-time/part-time). Comorbid conditions were Specific Conditions (SC) defined by the Agency for Healthcare Research and Quality (AHRQ). Subjects were classified as having the condition by any claims with an ICD-9 code for the SC.  The likelihood of being in the FD cohort was modeled using logistic regression with indicator (1/0) variables for 260 of the 261 specific AHRQ SCs (the FD-SC was not included).  Odds ratios >1.0 indicate the corresponding SC is more likely in the FD cohort, while ratios <1.0 indicate the SC is less likely to be in the FD cohort. RESULTS: The study dataset contained 85,119 employees (1669 with FD and 83,450 matched controls without FD). After controlling for all other AHRQ categories, the logistic regression found that 19 specific categories were more likely within the FD cohort, and 2 were less likely within the FD cohort.  Esophageal disorders, gastritis and duodenitis, abdominal pain, and gout were most associated with having FD (odds ratios of 3.8, 3.7, 3.6, and 2.5, respectively).  Only hypertension complications/secondary and disorders of teeth and jaw were significantly negatively associated with FD. CONCLUSIONS: This study identified varied comorbidities associated with FD diagnoses and may aid FD identification in future research.