Subcutaneous allergen immunotherapy (SCIT) has been shown to improve clinical course in children with asthma and allergic rhinitis (AR). Systemic and local side-effects may be seen during its administration. The purpose of this study was to evaluate risk factors associated with systemic and local side-effects in children receiving SCIT. We performed a retrospective chart review in the children who received allergen subcutaneous immunotherapy for asthma and/or allergen rhinitis. Demographic data, diagnosis, skin prick test results, presence of additional allergic diseases, the seasonal variation of adverse events in the first and third years of SCIT were recorded. A total of 508 eligible patients were included in the study. Mean age of the children was 10.9 +/- 3.2 years, and 65.4% were male. Asthma was present in 21.9% of the children, AR in 44.7%, 33.5% of them had both asthma and AR. According to the skin prick test results, sensitivity to more than one allergen was present in 45.1%, while the most common single-allergen sensitivities were to grass pollen and dermatophagoids (32.5% and 14.4%, respectively). Ratio of systemic and local side-effects was 4.7% and 9.3%, respectively. Local side-effects were more common than systemic reaction. SCIT is a safe treatment modality while using the appropriate dose and with the administration of dose-escalation protocol.