Changes in antimicrobial resistance of Escherichia coli among deployed U.S. military personnel being treated for diarrhea were evaluated. Stool samples were collected pretreatment and on days 7, 14, and 28 posttreatment. Resistance to ciprofloxacin was noted in 13.3% of baseline specimens, and rates of resistance against multiple antibiotics increased dramatically from baseline to day 7 and then tapered off to return to pretreatment levels by day 28, except for ciprofloxacin, suggesting that population accumulative usage of fluoroquinolones may result in an incremental increase in resistance rates.