This study analyzes prospectively the antibiotic prescription habits in terms of appropriateness of use and cost pattern effects in the paediatric wards of two different university hospital patient set-ups. Data on demographics, discharge diagnosis, antibiotic utilization and costs were collected prospectively from the childrens individual electronic charts at Rambam Health Care Campus (R) and Kaplan Medical Centre (K) in Israel. A total of 505 and 497 children from R and K units, respectively, were screened. Of the surveyed population, 239 and 330 children in the R and K units were hospitalized due to infectious diseases. The antibiotic appropriateness for the R and K units were 84% and 91%, respectively (p > 0.5). Total antibiotics Defined Daily Dose (DDD) and Drug Utilization 90% (DU90%) index were 241.7 and 217.5 for the R unit and 388 and 349.2 for the K unit, (p < 0.001). Drug Cost 90% indices (DC90%) for the two units were NIS 6,023.5 and NIS 5,955.8; respectively. This study generates up-to-date information on the antimicrobial prescription habits in two different hospitals and suggests that antibiotic treatment in both hospitals appears to be appropriate. Significant lower median antibiotic cost was depicted in the K admission unit in comparison to the R admission unit (11.3 NIS – 40.0 NIS; p < 0.01), respectively. Drug use evaluations are useful indicators for following trends of drug prescription, optimizing antibiotic usage and controlling expenditure.