Background and aims: To prevent urosepsis and reduce risk of renal scarring in children with urinary tract infection (UTI), empirical antibiotic treatment is started soon after the collection of urine specimens for culture and should be based on local epidemiology of uropathogens and their antimicrobial susceptibility. The aim of this study was to describe pathogens and their antimicrobial resistance in urine cultures of children under five, attending the Instituto de Medicina Integral Professor Fernando Figueira (IMIP), a teaching hospital in Recife, Brazil.Methods: cross sectional study comparing an earlier (January 1999 to August 2001) and a later (January to December 2008) period of time. It was recorded the urine culture positivity rate, pathogen species; antimicrobial resistance (Kirby-Bauer diffusion disks) of isolates in urine cultures of children with suspected UTI.Results: 601 (15%) of 4113 urine cultures were positive. The most frequent isolates in the earlier and later periods were, respectively: E.coli (30% and 41%), Klebsiella spp (27% and 25%), P aeruginosa (5% and 9%), P. mirabilis (7% and 7%) and Candida spp. (11% and 4%). In 2008, the resistance of E.coli was (in descending order): cotrimoxazole (68%), nalidixic acid (52%), cephalotin (30%), ciprofloxacin (15%) and nitrofurantoin (8%). When all pathogens are considered, the highest antimicrobial coverages would be reached by ciprofloxacin (88%, CI95%=83.4-91.6%) and nitrofurantoin (75%, CI95% = 68.6-80.5 %).Conclusions: Nitrofurantoin and ciprofloxacin remain viable alternatives, respectively for uncomplicated and complicated UTI. Trends of antimicrobial resistance should be monitored at the local level as important changes occur over time.