The contribution of viruses to lower respiratory tract disease in sub-Saharan Africa where human immunodeficiency virus may exacerbate respiratory infections is not well defined. No data exist on some of these viruses for Southern Africa. Comprehensive molecular screening may define the role of these viruses as single and co-infections in a population with a high HIV-AIDS burden. To address this, children less than 5 years of age with respiratory infections from 3 public sector hospitals, Pretoria South Africa were screened for 14 respiratory viruses, by PCR over 2 years. Healthy control children from the same region were included. Rhinovirus was identified in 33% of patients, RSV (30.1%), PIV-3 (7.8%), hBoV (6.1%), adenovirus (5.7%), hMPV (4.8%), influenza A (3.4%), coronavirus NL63 (2.1%), and OC43 (1.8%). PIV-1, PIV-2, CoV-229E, -HKU1, and influenza B occurred in <1.5% of patients. Most cases with adenovirus, influenza A, hMPV, hBoV, coronaviruses, and WU virus occurred as co-infections while RSV, PIV-3, and rhinovirus were identified most frequently as the only respiratory pathogen. Rhinovirus but not RSV or PIV-3 was also frequently identified in healthy controls. A higher HIV sero-prevalence was noticed in patients with co-infections although co-infections were not associated with more severe disease. RSV, hPMV, PIV-3, and influenza viruses had defined seasons while rhinovirus, adenovirus, and coronavirus infections occurred year round in this temporal region of sub-Saharan Africa. J. Med. Virol. 83:1458–1468, 2011. © 2011 Wiley-Liss, Inc.