Endothelial cells form the linchpin of vascular and lymphatic systems, creating intricate networks that are pivotal for angiogenesis, controlling vessel permeability, and maintaining tissue homeostasis. Despite their critical roles, there is no rigorous mathematical framework to represent the connectivity structure of endothelial networks. Here, we develop a pioneering mathematical formalism called $π$-graphs to model the multi-type junction connectivity of endothelial networks. We define $π$-graphs as abstract objects consisting of endothelial cells and their junction sets, and introduce the key notion of $π$-isomorphism that captures when two $π$-graphs have the same connectivity structure. We prove several propositions relating the $π$-graph representation to traditional graph-theoretic representations, showing that $π$-isomorphism implies isomorphism of the corresponding unnested endothelial graphs, but not vice versa. We also introduce a temporal dimension to the $π$-graph formalism and explore the evolution of topological invariants in spatial embeddings of $π$-graphs. Finally, we outline a topological framework to represent the spatial embedding of $π$-graphs into geometric spaces. The $π$-graph formalism provides a novel tool for quantitative analysis of endothelial network connectivity and its relation to function, with the potential to yield new insights into vascular physiology and pathophysiology.