The purpose of the study was to investigate the management of pyelonephritis in a large Italian pediatric population. A total of 1,333 patients (36% male) were considered. Escherichia coli was the most frequently isolated agent (89.9%), followed by Proteus mirabilis (3.6%) and Klebsiella oxytoca (2.1%). 27% of microorganisms were resistant to amoxicillin, 4% to amoxicillin/clavulanic acid, 11% to trimethoprim-sulfamethoxazole, 2.4% to gentamicin and less than 2% to ceftazidime. Despite this resistance pattern showing that oral antibiotics, such as amoxicillin/clavulanic acid, are effective in vitro as well as parenteral antimicrobials, a parenteral antibiotic was given initially to 756 (57.2%) children. A prophylactic regimen was started in 922 patients with a rate of reinfection during prophylaxis of 9.5%; a higher rate of reinfection was observed in patients with reflux (25%) compared to children without reflux (3%) (p < 0.0001). Vesicoureteral reflux was demonstrated in 30% of patients. The number of renal abnormalities detected by DMSA in patients with and without reflux was significantly different (p < 0.001). CRP was higher in patients with scars (p < 0.02). In conclusion, pyelonephritis represents a common disease with about 2,500 days of hospitalization per year in the Veneto Region where there is a pediatric population of about 800,000 under 15 years of age. The results of antimicrobial in vitro tests indicate that amoxillicin/clavulanic acid could represent the antibiotic of choice. The high frequency of malformations, observed even in children between 6 and 12 years of age, may suggest the need of an imaging study including DMSA scan and VCUG in all age groups.