Background: Ventilator-associated pneumonia (VAP) is one of the most common healthcare-related infections in pediatric and neonatal intensive care units. In the present study, due to the importance of prevention, early identification, and treatment of VAP, nasal and endotracheal microorganisms were determined in intubated patients admitted to the pediatric intensive care unit. Objectives: The present study aims to determine the nasal and endotracheal (ETT) microorganisms in pediatric patients with intubated VAP admitted to the pediatric intensive care unit (PICU). Methods: This cross-sectional two-group case-control study was conducted on 90 intubated patients: Sixty patients with VAP (30 nasal, 30 tracheal tubes) and 30 patients without VAP, hospitalized in the PICU department of Amir al Mominin Ali (AS) Hospital in Zabol, Iran, from March 2018 to December 2018. The criteria for diagnosing VAP was the clinical pulmonary infection score (CPIS). In both case and control groups, samples were collected from nasal tubes using nasal swabs and from tracheal tubes (ETT) as tracheal aspirates from intubated patients, and sent to the laboratory for culture. The collected samples were interpreted in the microbiology laboratory to identify microorganisms. Data collection was done using a demographic information questionnaire and the clinical pulmonary infection score CPIS. The data was entered into SPSS 20 statistical software and analyzed. Results: The results of the present study showed that gender and age of patients do not affect the incidence of VAP, but children with VAP have a significantly longer stay in the PICU. Microbiological examination showed that Klebsiella and Escherichia coli (13.3%) were the most frequent among the positive nasal samples, and Klebsiella and E. coli (36.7%) were the most frequent among the positive tracheal samples. The diversity of microbes observed in ETT samples was also higher. Conclusions: The present study showed that the duration of hospitalization in the pediatric intensive care unit, as well as the age of hospitalized patients, can increase the risk of VAP. Additionally, nasal sampling is effective in identifying and differentiating VAP patients. It is suggested to reduce the duration of hospitalization in these departments as much as possible and to pay more attention to older children to prevent the increase of VAP. The results indicate that nasal bacteria play a role in the more severe occurrence of ventilator-induced pneumonia. Therefore, it is recommended to use broad-spectrum antibiotics and implement preventive nursing measures. If possible, starting feeding earlier through a gastric tube is also suggested.