The purpose of this investigation was to collect information regarding rhinovirus (RV) circulation in children with lower respiratory tract infections (LRTIs) in Burundi, Central Africa. We enrolled all of the children aged between 1 month and 14 years who were admitted to the hospital of Kiremba, North Burundi, with fever and signs and symptoms of LRTI (i.e., cough, tachypnea, dyspnea or respiratory distress, and breathing with grunting or wheezing sounds with rales) between 1 November 2010 and 31 October 2011, and obtained nasopharyngeal swabs for RV detection by means of polymerase chain reaction (PCR). The VP4/VP2 region of the positive samples was sequenced to determine the species of RV (A, B, or C). Four hundred and sixty-two children were enrolled: 160 (34.6 %) with bronchitis, 35 (7.6 %) with infectious wheezing, and 267 (57.8 %) with community-acquired pneumonia (CAP). RV infection was demonstrated in 186 patients [40.3 %; mean age ± standard deviation (SD) 1.77 ± 2.14 years]. RV infection was detected in 78 patients aged <12 months (40.0 %), 102 aged 12-48 months (44.3 %), and six aged >48 months (16.7 %; p < 0.01 vs. the other age groups). The most frequently identified RV was RV-A (81 cases, 43.5 %), followed by RV-C (47, 25.3 %) and RV-B (18, 9.7 %); subtyping was not possible in 40 cases (21.5 %). RV-A was significantly associated with bronchitis and CAP (p < 0.01) and RV-C with wheezing (p < 0.05). In Burundi, RVs are frequently detected in children with LRTIs. RV-A seems to be the most important species and is identified mainly in patients with bronchitis and CAP.