Introduction. Urinary tract infection is common in childhood. Depending on the localization of the infection, severity of its clinical presentation and possible acute and long-term complications, it may be described as either acute cystitis or acute pyelonephritis. Objective. The aim of this study was to assess the resistance patterns of uropathogens during the last 5 years in newborns and young children with acute pyelonephritis. Methods. Uropathogens resistance to commonly usable anti-microbial agents (ampicillin, a combination of sulphamethoxasole and trimethoprim, cephalexin, ceftriaxone, cefotaxime, ceftazidime, gentamycin, amikacin, ciprofloxacin, imipenem and nalidixic acid) was retrospectively studied in newborns and young children treated during early (2005-2007) and late (2008-2009) study periods. Anti-bacterial susceptibility testing of the urine isolates was performed by the standard disc diffusion method. Results. 117 newborns and 294 children aged 9.3±0.7 months were treated during early (n=136) or late (n=275) study period due to the first episode of acute pyelonephritis. Escherichia coli was the most common bacterial pathogen (85.5%). Compared to children older than one month, newborns had higher degree of antibacterial resistance to 2nd and 3rd generation cephalosporins, aminoglycosides, and nalidixic acid during early, and to ceftazidime, aminoglycosides and nalidixic acid during late study period. Also, multidrug resistance was more common in newborns during the early study period. Conclusion. Newborns had higher rate of antibacterial resistance than young children. The progressive increase of anti-microbial resistance in children with acute pyelonephritis is of great concern.