Rationale: Human rhinovirus infections cause colds and trigger exacerbations of lower airway diseases. Objectives: To define changes in gene expression profiles during in vivo rhinovirus infections. Methods: Nasal epithelial scrapings were obtained before and during experimental rhinovirus infection, and gene expression was evaluated by microarray. Naturally-acquired rhinovirus infections, cultured human epithelial cells, and short interfering RNA (siRNA) knockdown were used to further evaluate the role of viperin in rhinovirus infections. Measurements: Symptom scores and viral titers were measured in subjects inoculated with rhinovirus or sham control, and changes in gene expression were assessed at 8 h and 48 h after inoculation. Real-time reverse transcription-polymerase chain reaction for viperin and rhinoviruses were used in naturally-acquired infections, and viperin mRNA levels and viral titers were measured in cultured cells. Main Results: Rhinovirus induced changes in gene expression were not observed at 8 h after viral infection, but 11, 887 gene transcripts were significantly altered in scrapings obtained 2 days post-inoculation. Major groups of upregulated genes included chemokines, signaling molecules, interferon-responsive genes and antivirals. Viperin expression was further examined and also was increased in naturally-acquired rhinovirus infections, as well as in cultured human epithelial cells infected with intact, but not replication-deficient, rhinovirus. Knockdown of viperin using siRNA increased rhinovirus replication in infected epithelial cells. Conclusions: Rhinovirus infection significantly alters expression of many genes associated with the immune response, including chemokines and antivirals. The data obtained provide insights into the host response to rhinovirus infection and identify potential novel targets for further evaluation.