Respiratory viruses discovered in the 21st century and human herpes viruses (N=13) were seldom (4/50) detected in our cystic fibrosis patients although exacerbation frequency (7.75+/-2.9/a versus 4.45+/-2.1/a; p=0.03) and colonization with Aspergillus fumigatus (RR: 2.6; CI95: 1.8-3.7), Pseudomonas aeruginosa (RR: 1.84; CI95: 1.4-2.4), and Staphylococcus aureus (RR: 1.5; CI95: 1.2-1.9) including MRSA (RR: 4.6; CI95: 1.3-16.6) were associated with virus positivity. Further studies should clarify whether this finding reflects non-specific colonization (human Bocavirus) or reactivation (Epstein-Barr virus) or rather an acceleration of lung tissue inflammation.