Evidence-based articles have demonstrated an increase in diabetes prevalence, but diabetes prevalence in the enrolled Military Health System population was previously understudied. Variability in diabetes prevalence rates calculated from 5 groups of algorithms was examined in the Military Health System population (3 million enrollees per year) from fiscal years 2006 to 2010. Time trend analysis and rate comparisons to the U.S. population were also performed. Increasing linear trends in diabetes prevalence from 2006 to 2010 were seen in all algorithms, though considerable rate variation was observed within each study year. Prevalence increased with age, except for a slight decrease in those ≥75 years. Overall diagnosed diabetes prevalence ranged from 7.26% to 11.22% in 2006 and from 8.29% to 13.55% in 2010. Prevalence among active duty members remained stable, but a significant upward trend was observed among nonactive duty members across study years. Age-standardized rates among nonactive duty females were higher than the U.S. population rates from 2006 to 2010. This study demonstrates prevalence rate variability because of differing case algorithms and shows evidence of a growing diabetes population in the Military Health System, specifically within the nonactive duty 45 years and older demographic groups. Further research of this population should focus on validation of case definitions.