A single-cell RNA sequencing analysis of 606,380 endothelial, perivascular, and other tissue-derived cells from 117 samples, including 68 human fetuses and adult patients, was conducted to construct a molecular atlas of the developing fetal, adult control, and diseased human brain vasculature. The study identified extensive molecular heterogeneity in the vasculature of healthy fetal and adult human brains and across five vascular-dependent central nervous system (CNS) pathologies, including brain tumors and brain vascular malformations. Pathological endothelial cells showed altered arteriovenous differentiation and reactivated fetal as well as conserved dysregulated genes and pathways. Pathological endothelial cells displayed a loss of CNS-specific properties and upregulated MHC class II molecules, indicating atypical features of CNS endothelial cells. Cell-cell interaction analyses predicted substantial endothelial-to-perivascular cell ligand-receptor cross-talk, including immune-related and angiogenic pathways, revealing a central role for the endothelium in brain neurovascular unit signaling networks. The study provides insights into the molecular architecture and heterogeneity of the developing, adult/control, and diseased human brain vasculature and serves as a powerful reference for future studies. The brain vasculature is crucial for both normal brain function and vascular-dependent CNS pathologies such as brain tumors, brain vascular malformations, stroke, and neurodegenerative diseases. Understanding the cellular and molecular mechanisms of the vasculature during brain development, in the healthy adult brain, and in vascular-dependent brain diseases has broad implications for biological understanding and therapeutic targeting of the pathological brain vasculature. Vascular growth and network formation, involving endothelial cells (ECs) and other cells of the neurovascular unit (NVU), are highly dynamic during brain development, almost quiescent in the healthy adult brain, and reactivated in various angiogenesis-dependent brain pathologies, including brain tumors and brain vascular malformations. The study reveals the molecular architecture and heterogeneity of the developing, adult/control, and diseased human brain vasculature, highlighting the importance of developmental pathways in vascular-dependent brain pathologies. The study also identifies AV zonation markers in brain ECs and shows that ECs in pathological conditions exhibit altered AV specification and CNS specificity. The study further reveals that pathological ECs upregulate MHC class II receptors, indicating atypical features of CNS endothelial cells. The study provides a comprehensive molecular atlas of the human brain vasculature, offering insights into the role of ECs in the brain neurovascular unit and their interactions with other cells. The study highlights the importance of ECs in the brain neurovascular unit and their role in signaling networks. The study also identifies the molecular signatures of different brain pathologies and their impact on the vasculature. The study provides a valuable resource for understanding the molecular mechanisms underlying brain vascular diseases and for developing therapeutic strategies.A single-cell RNA sequencing analysis of 606,380 endothelial, perivascular, and other tissue-derived cells from 117 samples, including 68 human fetuses and adult patients, was conducted to construct a molecular atlas of the developing fetal, adult control, and diseased human brain vasculature. The study identified extensive molecular heterogeneity in the vasculature of healthy fetal and adult human brains and across five vascular-dependent central nervous system (CNS) pathologies, including brain tumors and brain vascular malformations. Pathological endothelial cells showed altered arteriovenous differentiation and reactivated fetal as well as conserved dysregulated genes and pathways. Pathological endothelial cells displayed a loss of CNS-specific properties and upregulated MHC class II molecules, indicating atypical features of CNS endothelial cells. Cell-cell interaction analyses predicted substantial endothelial-to-perivascular cell ligand-receptor cross-talk, including immune-related and angiogenic pathways, revealing a central role for the endothelium in brain neurovascular unit signaling networks. The study provides insights into the molecular architecture and heterogeneity of the developing, adult/control, and diseased human brain vasculature and serves as a powerful reference for future studies. The brain vasculature is crucial for both normal brain function and vascular-dependent CNS pathologies such as brain tumors, brain vascular malformations, stroke, and neurodegenerative diseases. Understanding the cellular and molecular mechanisms of the vasculature during brain development, in the healthy adult brain, and in vascular-dependent brain diseases has broad implications for biological understanding and therapeutic targeting of the pathological brain vasculature. Vascular growth and network formation, involving endothelial cells (ECs) and other cells of the neurovascular unit (NVU), are highly dynamic during brain development, almost quiescent in the healthy adult brain, and reactivated in various angiogenesis-dependent brain pathologies, including brain tumors and brain vascular malformations. The study reveals the molecular architecture and heterogeneity of the developing, adult/control, and diseased human brain vasculature, highlighting the importance of developmental pathways in vascular-dependent brain pathologies. The study also identifies AV zonation markers in brain ECs and shows that ECs in pathological conditions exhibit altered AV specification and CNS specificity. The study further reveals that pathological ECs upregulate MHC class II receptors, indicating atypical features of CNS endothelial cells. The study provides a comprehensive molecular atlas of the human brain vasculature, offering insights into the role of ECs in the brain neurovascular unit and their interactions with other cells. The study highlights the importance of ECs in the brain neurovascular unit and their role in signaling networks. The study also identifies the molecular signatures of different brain pathologies and their impact on the vasculature. The study provides a valuable resource for understanding the molecular mechanisms underlying brain vascular diseases and for developing therapeutic strategies.