Background: Few studies have investigated the disease burden and genetic diversity of human rhinoviruses (HRVs) in developing countries. Objectives: To assess the burden of HRV in Amman, Jordan, and to characterise clinical differences between HRV groups. Study design: We prospectively studied children <5 years, hospitalised with respiratory symptoms and/or fever in Amman, Jordan. Viruses were identified by real-time reverse transcriptase polymerase chain reaction (RT-PCR). VP4/VP2 gene sequencing was performed on HRV-positive specimens. Results: Of the 728 enrolled children, 266 (37%) tested positive for picornaviruses, 240 of which were HRV. Of the HRV-positive samples, 62 (26%) were of the recently identified group HRVC, 131 (55%) were HRVA and seven (3%) were HRVB. The HRVC strains clustered into at least 19 distinct genotypes. Compared with HRVA-infected children, children with HRVC were more likely to require supplemental oxygen (63% vs. 42%, p = 0.007) and, when co-infections were excluded, were more likely to have wheezing (100% vs. 82%, p = 0.016). Conclusions: There is a significant burden of HRV-associated hospitalisations in young children in Jordan. Infection with the recently identified group HRVC is associated with wheezing and more severe illness.