Regulatory measures and public concerns regarding bisphenol A (BPA) have led to its replacement by structural analogues, such as BPAF, BPAP, BPB, BPF, BPP, BPS, and BPZ. However, these alternatives are under surveillance for potential endocrine disruption, particularly during the critical period of fetal development. Despite their structural analogies, these BPs differ greatly in their placental transport efficiency. For predicting the fetal exposure of this important class of emerging contaminants, quantitative structure-activity relationship (QSAR) studies were developed to model and predict the placental clearance indices (CI). The most usual input parameters were molecular descriptors obtained by modelling, but for bisphenols (BPs) with structural similarities or heteroatoms such as sulfur, these descriptors do not contrast greatly. This study evaluated and compared the capacity of QSAR models based either on molecular or chromatographic descriptors or a combination of both to predict the placental passage of BPs. These chromatographic descriptors include both the retention mechanism and the peak shape on columns that reflect specific molecular interactions between solute and stationary and mobile phases and are characteristic of the molecular structure of BPs. The chromatographic peak shape such as the asymmetry and tailing factors had more influence on predicting the placental passage than the usual retention parameters. Furthermore, the QSAR model, having the best prediction capacity, was obtained with the chromatographic descriptors alone and met the criteria of internal and cross validation. These QSAR models are crucial for predicting the fetal exposure of this important class of emerging contaminants.