Medical follow-up and systematic nasal swabbing were performed pre-and post-Hajj. Additional samples were obtained per-Hajj, at symptom onset in ill pilgrims. Viruses were identified using the BioFire FilmArray ® Respiratory multiplex qualitative PCR panel. Results: 109 pilgrims were included. 83.5% presented respiratory symptoms during Hajj and 39.5% were still symptomatic on return. 5.5% of pre-Hajj, 95.2% of per-Hajj (at symptom onset) and 46.5% of post-Hajj samples tested positive (p < 0.0001). Acquisition rates of rhinovirus/enterovirus, coronavirus 229E and influenza A virus were respectively 38.6%, 19.8% and 2.0%. Although rhinovirus/enterovirus, coronavirus 229E and influenza A clearance were respectively 70.6%, 71.4% and 100% on return, overall virus carriage proportion on return was 75.0% in pilgrims with influenza-like illness and 44.0% in those who have never experienced this symptoms or resolved it (OR = 4.05, 95% CI [1.02-16.02]). Conclusions: Viruses likely play some role in the pathogenesis of the respiratory tract infections at the Hajj. Point of care-rapid multiplex PCR assays are valuable diagnosis tools in this context when used at respiratory symptom onset or soon after.