Robustness is a prominent feature of most biological systems. In a cell, the structure of the interactions between genes, proteins, and metabolites has a crucial role in maintaining the cell's functionality and viability in presence of external perturbations and noise. Despite advances in characterizing the robustness of biological systems, most of the current efforts have been focused on studying homogeneous molecular networks in isolation, such as protein-protein or gene regulatory networks, neglecting the interactions among different molecular substrates. Here we propose a comprehensive framework for understanding how the interactions between genes, proteins and metabolites contribute to the determinants of robustness in a heterogeneous biological network.We integrate heterogeneous sources of data to construct a multilayer interaction network composed of a gene regulatory layer, and protein-protein interaction layer and a metabolic layer. We design a simulated perturbation process to characterize the contribution of each gene to the overall system's robustness, defined as its influence over the global network. We find that highly influential genes are enriched in essential and cancer genes, confirming the central role of these genes in critical cellular processes. Further, we determine that the metabolic layer is more vulnerable to perturbations involving genes associated to metabolic diseases. By comparing the robustness of the network to multiple randomized network models, we find that the real network is comparably or more robust than expected in the random realizations. Finally, we analytically derive the expected robustness of multilayer biological networks starting from the degree distributions within or between layers.These results provide new insights into the non-trivial dynamics occurring in the cell after a genetic perturbation is applied, confirming the importance of including the coupling between different layers of interaction in models of complex biological systems.The recent development of high throughput omics technologies has facilitated the extensive profiling of the different molecular strata composing living organisms, such as the transcriptome, epigenome, and proteome, providing a more comprehensive picture of the detailed molecular composition of cellular systems. However, cellular processes are not only driven by individual molecules but also by the interplay between them. These interactions are conventionally modeled as context-specific molecular interaction networks [1], such as gene regulatory networks [2], protein-protein interaction (PPI) networks [3], and metabolic networks [4,5]. Such network-based analysis [6] has become an effective and widely used tool in the analysis of cellular systems. While the study of the static topology of these networks has been successful in various applications, such as disease gene prioritization [7][8][9], disease biomarkers discovery [10], and disease diagnosis and subtyping [11], substantial insights can be gained by analyzing the properties of d...