The carriage of bacterial pathogens in the human upper respiratory tract (URT) is associated with a risk of invasive respiratory tract infections, but the related epidemiological information on this at the population level is scarce in Malaysia. This study aimed to investigate the URT carriage ofStreptococcus pneumoniae,Haemophilus influenzae,Neisseria meningitidis,Staphylococcus aureus,Klebsiella pneumoniaeandPseudomonas aeruginosaamong 100 university students by nasal and oropharyngeal swabbing. The presence ofS. aureus,K. pneumoniaeandP. aeruginosawas assessed via swab culture on selective media and PCR on the resulting isolates. ForS. pneumoniae,H. influenzaeandN. meningitidis, their presence was assessed via multiplex PCR on the total DNA extracts from chocolate agar cultures. The carriage prevalence ofH. influenzae,S. aureus, S. pneumoniae,K. pneumoniae, N. meningitidisandP. aeruginosaamong the subjects was 36%, 27%, 15%, 11%, 5% and 1%, respectively, by these approaches. Their carriage was significantly higher in males compared to females overall. TheS. aureus,K. pneumoniaeandP. aeruginosaisolates were also screened by the Kirby-Bauer assay, in which 51.6% ofS. aureuswere penicillin-resistant. The outcomes from carriage studies are expected to contribute to informing infectious disease control policies and guidelines.