OBJECTIVE: In patients with severe or refractory juvenile dermatomyositis (JDM), second-line treatments may be required. Cyclophosphamide (CYC) is used to treat some connective tissue diseases, but evidence of efficacy in JDM is limited. This study aimed to describe clinical improvement in JDM patients treated with CYC and model efficacy of CYC compared to patients not treated with CYC. METHODS: Clinical data on skin, global and muscle disease were analyzed from patients recruited to the Juvenile Dermatomyositis Cohort and Biomarker Study. Clinical improvement following CYC treatment was described using unadjusted analysis. Marginal structural models (MSMs) were used to model treatment efficacy and adjust for confounding by indication. RESULTS: Compared to CYC start, there were reductions at 6, 12 and 24 months in skin disease (p=1.3×10-10 ), global disease (p=2.4×10-8 ), and muscle disease (p=8.0×10-10 ) for n=56 patients treated with CYC in unadjusted analysis. Limited evidence suggested reduction in glucocorticoid dose (p=0.047) in patients treated with CYC. MSM analysis showed reduced global disease and skin disease in patients who started CYC treatment over 12 months ago compared to patients never or not yet treated with CYC. In these patients, modified disease activity score for skin disease was 1.19 units lower (p=0.0085) and physician's global assessment was 0.66 units lower (p=0.027). Minor adverse events were reported in 3 patients within 1 year of stopping CYC. CONCLUSION: CYC is efficacious with no short-term side-effects seen in this study. Improvements in skin, global and muscle disease were observed. Further studies are required to evaluate longer-term side-effects. This article is protected by copyright. All rights reserved