Recommendations for low-dose cone-beam computed tomography (LD-CBCT) protocols for pediatric image-guided radiation therapy (IGRT) are lacking. We aim to evaluate the precision of two LD-CBCT protocols to align to bone and soft tissue landmarks for pediatric patients receiving IGRT to the abdomen and pelvis (A/P). 858 CBCTs from 46 pediatric patients who received IGRT to the A/P starting January 2015 –December 2017 were reviewed. Image quality of CBCTs over this time guided the development of two significantly dose-reduced protocols, LD-CBCT1 (180º rotation, 120 kV, 63 mAs total, 315 frames, S20 collimator) and LD-CBCT2 (180º rotation, 100 kV, 31.5 mAs total, 315 frames, S20 collimator). Eight patients with at least 1 CBCT from both protocols during the course of IGRT were selected for a simulation study, and a representative LD-CBCT1 and LD-CBCT2 scan was registered to the simulation CT (sim-CT) separately aligning to bone and soft tissue. To simulate the process of correcting a setup error to a bone and soft tissue landmark using each protocol, 18 blinded random offsets (max translation 10 mm any x/y/z direction) were applied to each LD-CBCT1 and LD-CBCT2 from a starting registration to bone and a soft tissue structure. Each of the resultant 504 simulated set-up errors was then blindly corrected using rigid registration by a radiation oncologist. The vector magnitude difference (VM= √(x2 + y2 + z2)) between the random offset and final registration attempt was calculated, adjusting for any systematic error in the initial sim-CT↔LD-CBCT1/2 registration. A one-sided paired T-test was used to evaluate if LD-CBCT1, delivering higher dose, was superior to the lower dose LD-CBCT2 for bone and soft tissue alignment.. Age and patient size (using abdominal area) ranges of the eight sample patients with representative LD-CBCT1 and LD-CBCT2 scans were 1-5-9.2 years and 516-954 cm2, respectively. Comparing 288 registrations to a bone landmark across 8 patients, there was no difference in the vector magnitude of the offsets using LD-CBCT 1 (mean [̄x̄], 0.73 mm; standard deviation [σ], 0.39 mm) and LD-CBCT2 (̄x̄, 0.74 mm; σ, 0.40 mm) (p=0.425). Comparing 216 registrations to a soft tissue landmark across 6 patients, alignment using LD-CBCT2 (̄x̄, 1.55 mm; σ, 1.08 mm) resulted in larger differences in the vector magnitude of the offsets compared to LD-CBCT1 (̄x̄, 1.37 mm; σ, 0.74 mm) (p=0.049). Given the particular importance of reducing dose to normal tissue in pediatric patients and the increasing use of IGRT, clinics treating pediatric patients should consider a protocol mirroring LD-CBCT2 validated in this study for A/P IGRT aligned to bone. Delivering higher dose, LD-CBCT1 was slightly superior to LD-CBCT2 for soft tissue alignment, but further investigation is needed given that this study design evaluated the utility in alignment to a kidney structure as the representative soft tissue structure.