Purpose: In this study, it was aimed to compare the types of significant bacteriuria and antibiotic resistance characteristics in children with myelodysplasia-neurogenic bladder in whom clean intermittent catheterization (CIC) and children with normal bladder and recurrent urinary tract infection. Material and methods: The patients who had neurogenic bladder due to spinal dysraphism with clean intermittent catheterization were called group 1 and, the children with recurrent urinary tract infection without neurogenic bladder were group 2. In addition, group 1 patients were divided into two subgroups according to the presence of vesicoureteral reflux, and all groups were compared in terms of microorganism species and antibiotic resistance. Results: Ninety-nine of the urine cultures obtained from 26 patients (mean age 6.01±4 years, 18 girls) produced significant bacteria in Group 1 within one year, 352 urine cultures obtained from 26 patients (mean age 7.2±4.34 years, 56 girls) in group 2 showed significant bacteria grown. E. coli was the most common microorganism in both groups. The ratio of extended-spectrum beta-lactamase microorganisms (ESBL +) in Group 1 were higher than in Group 2. Non E. Coli microorganisms such as Klebsiella were found highest rate in children with neurogenic bladder who were using prophylactic antibiotic. The resistances to ampicillin, ceftriaxone and gentamicin were high in this group. Conclusion: The use of prophylactic antibiotics may lead to the development of drug-resistance in patients with neurogenic bladder in whom clean intermittent catheterization. Therefore use of prophylactic antibiotics this group may not be necessary. Highest antibiotic resistance was found in the patients with normal bladder and vesicoureteral reflux. Also a significant increase renal scar incidence in same group. We suggest that prophylactic antibiotics should not be used in patients with neurogenic bladder who used CIC.