Children performing clean intermittent catheterisation (CIC) have a higher risk of bacteriuria. This occasionally can lead to full urinary tract infection (UTI) which can influence long-term renal function. Hydrophilic catheters are said to be less traumatic to the urothelium and should therefore reduce bacterial translocation or UTIs. This study looked at 50 patients with myelomeningocele who were undergoing CIC and who were prospectively randomised during an investigator blinded study to 25 hydrophilic catheter usage and 25 PVC catheter usage. Urine cultures were collected at enrolment, and at three, six, and twelve months, and bacterial species were designated as pathogenic or non-pathogenic. Of interest was that a total of 232 different bacterial isolates were collected from 182 urine specimens. E Coli was the most predominant. Sixteen percent had no bacterial growth. Hydrophilic catheters had non-statistically significant less average number of pathogenic species (0.81 per urine sample) vs. PVC catheters (1.24 per urine sample). The study population demonstrated a trend in reduced recovery of potentially pathogenic bacteria when using hydrophilic catheters.