Abstract: Complex networks are often compared using selected graph-theoretical measures that capture a selected set of properties with effects ranging from local to global, such as degree, clustering or betweenness centrality. Here we introduce a structural fingerprinting framework based on graphlets: small rooted subgraphs whose distributions provide a systematic description of local-to-mesoscale topology. Across synthetic networks generated from several random graph models, graphlet fingerprints capture parameter-dependent structural differences, outperform standard graph-theoretical measures, and identify even subtle local patterns driving discrimination. We then apply the framework to empirical resting-state functional connectomes, documenting that while graphlets show superior sensitivity also to controlled topological perturbations of brain connectivity, specifically in schizophrenia-control classification they perform only comparably to classical graph-theoretical features. This is in line with the notion that schizophrenia-related alterations are dominated by spatially localized connectivity changes rather than general topological reorganization. Altogether, the generative modeling, targeted perturbations and real-world neuroimaging classification challenge position graphlets as flexible structural fingerprints of complex networks, while carefully outlining their strength and weaknesses compared to more classical graph theoretical features.