BACKGROUND: Basophils are important mediators in the pathobiology of atopic diseases, yet the heterogeneity of basophils within the perinatal environment remains incompletely understood. In our study, we aimed to perform comprehensive profiling of paired maternal and cord blood basophils using a single-cell omics approach to look into their distinct transcriptional signatures. METHODS: Basophils were isolated from four paired maternal-cord blood samples at the time of delivery, including one mother who delivered monozygotic twins. Basophil characterization of maternal blood (MB) and cord blood (CB) was analyzed in flow cytometry. Single cell RNA sequencing (scRNA-seq) was performed to further examine the basophils composition and heterogeneity in MB and CB. RESULTS: We observed that CB basophils have lower expression of FCER1A, and no cell-bound or circulating IgE levels as compared to MB. Our scRNA-seq data show that MB and CB basophils are different in both transcriptomic and functional profiles. CB basophils exhibit greater heterogeneity than MB. Low interindividual variability between twin CB basophil samples confirmed that the transcriptomic difference between MB and CB basophils is biologically meaningful. Trajectory pseudotime analysis revealed that CB basophils have an earlier pseudotime, potentially indicating a more naïve state. In addition, we demonstrated that CB basophils exhibit distinct functional capacities. CONCLUSION: Our data identified protein and gene signatures in MB and CB basophils. We demonstrated that CB has greater heterogeneity than MB basophils, thereby highlighting the relevance of single cell profiling of basophils in the context of the maternal-fetal interface.