Background: urinary tract infections (UTIs) with non-Escherichia coli (E. coli) species are associate with urological abnormalities. Objectives: To compare the prevalence of non-E. coli infections in patients with urological anomalies, neurogenic bladder dysfunction, and those with apparently normal urinary systems. Methods: Pediatric nephrology clinic at a tertiary-care center in east of Iran. Children affected by UTI enrolled from 2003 to 2016. The results of urine culture were noted at enrolment. Cases with nephrolithiasis who had normal voiding cystourethrogram were excluded. After the implementation of imaging and urodynamic examinations, 832 patients enrolled according to the following inclusion criteria: cases with vesicoureteral reflux, urinary obstruction, neurogenic bladder, and patients with apparently normal urinary tract. The prevalence of infections with E. coli vs. non-E. coli pathogens were compared between different groups of enrolled cases. Results: In this study, 62. 26% of the subjects had a normal urinary system, while 33. 77%, 3. 97%, and 2. 4% of whom had vesicoureteral reflux, neurogenic bladder, and obstruction, respectively. Non-E. coli pathogens were responsible for infections in 17. 29%, 19. 39%, 33. 74%, and 17. 15% of these cases, respectively. infections with non-E. coli pathogens were significantly more prevalent in cases with neurogenic bladder (P = 0. 003). Pseudomonas species were responsible for 4/125, 5/118, 5/28, and 0/6 episodes of non-E. coli infections in cases with apparently normal urinary system, patients with vesicoureteral reflux, cases with neurogenic bladder, and those with urinary obstruction, respectively (P = 0. 004). Conclusions: infections with non-E. coli and also Pseudomonas species are significantly more prevalent in patients with neurogenic bladder dysfunction rather than those with urological abnormalities and/or cases with apparently normal urinary system.