Objective To analyze the bacterial distribution and resistance in upper urinary tract stone patients, then choose suitable antibiotics and reduce infectious complications accordingly.Methods Middle flow urine, infectious stone and the end of kidney drainage tube were taken for culture in 148 patients who underwent percutaneous nephrolithotomy between January 2009 to September 2010. Antibiotics were used according to the culture results and the complications secondary to infection were analyzed. Results Urinary pathogens presented in 38 (25.7%) patients before operation.There were 112 strains of bacteria. The predominant strains included: Escherichia coli (17 cases,11.5%), Staphylococcus epidermidis (4 cases) and Proteus mirabillis (4 cases). Escherichia coli and Proteus mirabillis were common in stone culture. Staphylococcus epidermidis (5 cases),Pseudomonas aeruginosa (5 cases) and Staphylococcus haemolytcus (5 cases) were found in renal drainage tube culture which were positive in 25 patients. Imipenem, cefepime, vacomycin, nitrofurinton were sensitive and commonly used antibiotics. Forty-one patients (27.7 %) had fever postoperatively, including 10 positive for middle urine culture and 9 positive for drainage tube culture. One infective shock was diagnosed postoperatively. Conclusions Gram-negative bacilli are predominant in the upper urinary tract stone patients preoperatively. Gram-positive ones are common postoperatively.Suitable antibiotics, based on middle flow urine culture, could reduce urinary infective complications.