Objective: Circulating free nucleic acids are found at low levels in healthy subjects and in some diseases. The source is reported to be apoptosis of lymphocytes and other nucleated cells. The aim of this study is to investigate cfDNA levels in children with Henoch Schonlein purpura (HSP) during acute and remission phases. Methods: We investigated cfDNA levels in 21 children with HSP in acute phase and 21 in remission and in 25 healthy controls using real-time quantitative PCR. Results: We found significantly increased cfDNA levels in acute HSP patients (median: 6632.5 pg/ml) compared to those in remission (4540.8 pg/ml) and healthy controls (4650 pg/ml) (p<0.05). Conclusion: Significantly increased cfDNA levels in acute phase of HSP might be explained by increased apoptosis. Measuring cfDNA levels may have a potential role for monitoring HSP activity. For this finding, determination of complex interactions at cellular level and prognostic significance need further research.