Insulin resistance (IR) in liver, adipose and muscle tissue is a primary risk factor for metabolic diseases such as type 2 diabetes (T2D). A number of distinct environmental perturbations induce IR. However, it is unclear how these cause IR and whether these insults converge upon a common target or if IR can be induced through multiple pathways. To address this question we have undertaken an integrated systems analysis of IR 3T3-L1 adipocytes. These models represent perturbations known to induce IR in vivo, including incubation with 10 nM insulin for 24 h, 20 nM dexamethasone for 8 d or 2 ng/mL TNF-α for 4 d. In each model we assessed changes in the transcriptome by microarray and proteome by SILAC-based mass spectrometry. To identify points of convergence we performed integrated pathway analysis. This analysis identified several pathways to be dysregulated across multiple models. The cholesterol biosynthesis pathway was dysregulated in all models. At the protein level, cholesterogenic enzymes were up-regulated in response to chronic incubation with insulin, but down-regulated in response to TNF-α and dexamethasone. Membrane cholesterol levels were altered in line with changes in protein expression. To establish whether targeting cellular cholesterol may alleviate IR we pharmacologically manipulated its biosynthesis. In each model we were able to significantly improve insulin-stimulated glucose transport. Analysis of transcript data from adipose tissue from insulin resistant mice and humans revealed the cholesterol biosynthesis pathway to be up-regulated. In mice this was accompanied by increased membrane cholesterol levels. These data indicate that altered cellular cholesterol content contributes to insulin resistance in adipose tissue.