Objective: To evaluate the justification for the use of antimicrobial agents and to verify the possibility of its misuse among inpatient neonates. Methods: A cross-sectional 1-day study was conducted. Two questionnaires A and B relating to inpatient neonates were filled by registrars working in the four neonatal units of the main regional hospitals (Maternity, Farwaniya, Adan, and Jahra). The objectives of the study were not revealed to the registrars. Results: Of the 119 patients, 57 (48%) were on antimicrobial agents, and the cultures yielded positive in 25/57 (44%). The organisms were reported not to be susceptible to the antimicrobial agents in use in 19/25 (76%) of the cases, but it was continued in 4/19 (21%). Antimicrobial agents were also continued in another 9/32 (28%) despite negative culture results. Conclusion: Misuse of antimicrobial agents was homogeneously observed at various levels in all neonatal units. This implies that urgent action should be taken to overcome this problem.