Vancomycin and methicillin-resistant Staphylococcus aureus (VMRSA) is one of the important emerging pathogens worldwide that pose a challenge to a wide range of diseases in humans and animals. It is responsible for causing nosocomial and community infections, but it has also been reported to cause livestock infections. The aim of the study was to investigate the occurrence of vancomycin- and methicillin-resistant S. aureus in baby chicks with omphalitis in Egypt. Out of a total of 200 chicks, 10 isolates were recognized as S. aureus by microbiological and molecular methods. All S. aureus isolates were subjected to in vitro antimicrobial susceptibility testing against 12 antimicrobial agents by the disc diffusion method. Isolates revealed 100% resistance to clindamycin, methicillin, and amoxicillin, followed by azithromycin and quinupristin/dalfopristin (81.8%). Whereas, perceptible resistance was observed against sulfamethoxazole/trimethoprim, erythromycin, Linezolid, and tetracycline, with a percentage of 72.7%. Conversely, there is a higher sensitivity to gentamycin and ciprofloxacin, with percentages of 27% for each. The MIC results of vancomycin did not display inhibition of the growth of the tested isolates. Vancomycin had high MIC values of 64 μg/ml against all tested S. aureus isolates, which exhibited MIC values of 32 μg/ml. All isolates were found to be multidrug-resistant (MDR), indicating that they were resistant to at least three different classes of antibiotics. Molecular detection for the antibiotic resistance gene revealed that the mecA gene was detected in (10/11) isolates of S. aureus with a percentage of 90.9% which is responsible for methicillin resistance. None of the isolates contained mecC gene. Amplification of Spa virulence gene by using PCR showed that all isolates were positive for spa gene with a percentage of (100%). Furthermore, van A gene was detected in (6/11) isolates (54.4%), and van B was detected in 5/11 isolates with a percentage of 45.5%. The findings of this study confirm the presence of multi-drug resistant organisms in chicks. It significantly points to the great need to evaluate and monitor the incidence rate of multi-drug resistant organisms. The presence of VMRSA in poultry meat is of great concern for public health. Strict supervision and enforcement of laws to control the antibiotic usage in the food chain within established safe levels must be followed.