Osteoporosis is increasingly being recognized in children, mostly secondary to systemic underlying conditions or medication. However, no imaging modality currently provides a full evaluation of bone health in children. We compared DXA, a radiographic bone health index (BHI (BoneXpert) and cone-beam CT for the assessment of low bone mass in children with juvenile idiopathic arthritis (JIA). Data used in the present study was drawn from a large multicentre study including 228 children aged 4-16years, examined between 2015 and 2020. All had a radiograph of the left hand, a DXA scan and a cone-beam CT of the temporomandibular joints within four weeks of each other. For the present study, we included 120 subjects, selected based on DXA BMD and BoneXpert BHI to secure values across the whole range to be tested. One hundred and twenty children (60.0% females) were included, mean age 11.6years (SD 3.1years). There was a strong correlation between the absolute values of BHI and BMD for both total body less head (TBLH) (r = 0.75, p < 0.001) and lumbar spine (L1-L4) (r = 0.77, p < 0.001). The correlation between BHI standard deviation score (SDS) and BMD TBLH Z-scores was weak (r = 0.34) but significant (0 = 0.001), varying from weak (r = 0.31) to moderate (r = 0.42) between the three study sites. Categorizing BHI SDS and DXA BMD Z-scores on a 0-5 scale yielded a weak agreement between the two for both TBLH and LS, with w-kappa of 0.2, increasing to 0.3 when using quadratic weights. The agreement was notably higher for one of the three study sites as compared to the two others, particularly for spine assessment, yielding a moderate kappa value of 0.4 - 0.5. For cone-beam CT, based on a 1-3 scale, 59 out of 94 left TMJ's were scored as 1 and 31 as score 2 by the first observer vs. 87 and 7 by the second observer yielding a poor agreement (kappa 0.1). Categorizing DXA LS and automated radiographic Z-scores on a 0-5 scale gave a weak to moderate agreement between the two methods, indicating that a hand radiograph might provide an adjuvant tool to DXA when assessing bone health children with JIA, given thorough calibration is performed.