The daily use of Trimethoprim-Sulfamethoxazole (TMP-SMX) prophylaxis reduces morbidity and mortality among patients infected with Human Immunodeficiency Virus (HIV) but its impact on increasing antimicrobial resistance rates has been a concern. Escherichia coli, a member of the human intestinal flora and a common cause of UTI is normally susceptible to TMP-SMX but increasing resistance to TMP-SMX has been reported. This study was set out to assess the effect of daily TMP-SMX prophylaxis antimicrobial resistance rates of Escherichia coli from the intestinal flora of HIV-infected patients and identify the risk factors for resistance. HIV-infected patients were enrolled into two groups. In the first group a cross-sectional study was carried out to get a broad overview of the prevalence of resistance to TMP-SMX at different points in time. In the second group, a cohort study was done to confirm the first study and evaluate the trend in the development of resistance over time as well as risk factors. Feacal isolates from the 550 patients were tested in the cross sectional study. Two hundred of these were new patients who had not commenced prophylaxis. The rest were patients who had been on TMP-SMX prophylaxis for 3, 6, 9, and 12 months. 1 For cohort study, 120 control patients were further followed up for 12 months to determine the rate of development of resistance. There was a baseline resistance rate of 54%. This had risen to 80% at 3 months and all isolates were resistant by 12 months. The cohort showed 23.9% increase in resistance from 54% to 77.9% in first 3 months, rising to 96.1% by 6 months and all isolates were resistant by 9 months.There was also evidence of cross resistance to other antibiotics with significant association between TMP-SMX resistance (p<0.0001). Ampicillin showed 8.6% increase in resistance from 74% to 82.6% in first 3 months, rising to 98.3% by 6 months, 99.4% by 9 months and all isolates were resistant by 12 months. Augmentin showed 15.2% increase in resistance from 32.5% to 47.7% in first 3 months, rising to 76.1% by 6 months, 86.3% by 9 months and all isolates were resistant by 12 months. Ceftriaxone showed 8.8% increase in resistance from 2.0% to 10.8% in first 3 months, rising to 20.6% by 6 months, 24.2% by 9 months and 54.3% by 12 months. Genticin showed 1.3% decrease in resistance from 7.5% to 6.2 in first 3 months, rising to 13.9% by 6 months, 22.4% by 9 months and 32.5% by 12 months while Ciprofloxacin showed 5.9% increase in resistance from 12.0% to 17.9% in first 3 months, rising to 26.7% by 6 months, 62.1% by 9 months and 82.1% by 12 months. Risk factors for resistance include the use of Ampiclox and Sulfadoxine-Pyrimethamine among the patients. There was significant association between the use of these antimicrobials and TMP SMX resistance (p< 0.001) in the preceeding month. In conclusion, the carriage rate of feacal E. coli resistant to TMP-SMX is common before TMP SMX prophylaxis. Initiation of TMP-SMX leads to further increase in resistance to TMP-SMX and cross-resistance to other antimicrobials. This study further suggests that that these patients are 2 at higher risk of having E. coli infections and possibly infections from other enterobacteriaceae as a result of multi-resistant organisms. Secondly, findings show that these patients can be a source of antibiotic resistant organisms in the hospital and the community.