Angiogenesis is a complex multicellular process requiring the orchestration of many events including migration, alignment, proliferation, lumen formation, remodeling and maturation. Such complexity indicates that not only individual genes but also entire signalling pathways will be crucial in angiogenesis. In order to define an angiogenic blueprint of regulated genes, we utilized our well characterized 3D collagen gel model of in vitro angiogenesis, in which the majority of cells synchronously progress through defined morphological stages culminating in the formation of capillary tubes. We developed a comprehensive three tiered approach using microarray analysis which has allowed identification of genes known to be involved in angiogenesis, genes hitherto unlinked to angiogenesis as well as novel genes, and has proven especially useful for genes where the magnitude of change is small. Of interest is the ability to recognize complete signalling pathways which are regulated and genes clustering into ontological groups implicating the functional importance of particular processes. We have shown that consecutive members of the mitogen activated protein kinase (MAPK) and leukemia inhibitory factor (LIF) signalling pathways are altered at the mRNA level during in vitro angiogenesis. Thus, at least for the MAPK pathway, mRNA changes as well as the phosphorylation changes of these gene products may be important in the control of blood vessel morphogenesis. Furthermore, in this study, we demonstrate the power of virtual northern blot analysis, as an alternative to quantitative reverse transcription polymerase chain reaction (Q-RT-PCR), for measuring the magnitudes of differential gene expression.