Digital breast tomosynthesis (DBT) system is a novel imaging modality which is strongly depended on the performance of a detector. Recently, effective detective quantum efficiency (eDQE) has been introduced to solve the disadvantages of conventional DQE evaluations which do not consider clinical operating conditions. For eDQE evaluation, the variety of patient breast, especially the glandularity and thickness needs to be studied to consider different races of patient. For these reasons, eDQE in a prototype DBT system considering different breast thickness and glandularity was evaluated. In this study, we used the prototype DBT system with CsI(Tl) scintillator/CMOS flat panel digital detector developed by Korea Electrotechnology Research Institute (KERI). A scatter fraction, a transmission factor, an effective modulation transfer function (eMTF) and an effective normalized noise power spectrum (eNNPS) were measured in different thickness and glandularity of breast equivalent phantom. As results, scatter fraction increased and transmission fraction decreased by a factor of 2.09 and 6.25, respectively, as increasing glandularity and thickness. We also found that the breast phantom with small thickness presented high eMTF and low eNNPS. As results, eDQE from 4 cm thick breast phantom with 30% and 70% glandularity showed small changes from 0.20 to 0.19 at 0.1 mm-1, whereas eDQE from 50% glandularity of 3 cm and 5 cm presented relatively significant increase from 0.16 to 0.20 at 0.1 mm-1 spatial frequency. These indicated that eDQE was strongly affected by phantom thickness, but the effect of glandularity seemed to be trivial. According to our study, the whole system evaluation considering the races of patients from standard to abnormal cases is needed to be studied in future works.