Background Increased intraepithelial lymphocytosis (IEL) with preserved villous architecture is a common yet nonspecific finding on duodenal biopsies. Objective To study the change in frequency of isolated IEL on duodenal biopsy over time and determine whether previously reported disease associations have changed during that period. Design Retrospective study. Setting Single tertiary-care referral center. Patients Adults with a duodenal biopsy that showed normal villi and increased number of intraepithelial lymphocytes. Intervention Duodenal biopsy. Comprehensive electronic medical record search from January 1, 2000 through December 31, 2010. Main Outcome Measurements Demographic and clinical information. Results Of the 15,839 duodenal biopsies performed during the study period, 1105 (7.0%) had the histologic finding of interest. The odds of finding newly diagnosed celiac disease (CD) decreased by 0.9 on average during each year, whereas the odds of finding a non-celiac association increased by 1.12 times each year. Isolated increased IEL attributed to nonsteroidal anti-inflammatory drug (NSAID) use and small-intestine bacterial overgrowth (SIBO) increased by 1.06 and 1.3 times, respectively, for each year on average. Limitations Retrospective design, single center. Conclusion During the years 2000 through 2010, there has been an increased frequency with which duodenal biopsies were noted to have isolated increased IEL. The odds of a diagnosis of CD accounting for this finding have been decreasing, whereas the odds of NSAID use and SIBO have been increasing. Although the finding of isolated increased IEL on duodenal biopsy warrants work-up for CD in all patients, further investigation for other possible causes, including NSAID use and SIBO, should be considered as well.