Osteoblast cells synthesize collagen-rich ECM (extracellular matrix) in response to various environmental cues, but little is known about ECM-dependent variations in phosphorylation patterns. Using MC3T3 E1 osteoblast-like cells and mouse whole-genome microarrays, we investigated molecular signalling affected by collagen-based ECMs. A genome-wide expression analysis revealed that cells grown in the 3D collagen matrix partially suppressed the genes associated with cell adhesion and cell cycling. Western analysis demonstrated that the expression of the active (phosphorylated) form of p130Cas, FAK (focal adhesion kinase) and ERK1/2 (extracellular-signal-regulated protein kinase 1/2) was reduced in cells grown in the 3D matrix. Conversely, phosphorylation of p38 MAPK (p38 mitogen-activated protein kinase) was elevated in the 3D matrix, and its up-regulation was linked to an increase in mRNA levels of dentin matrix protein 1 and bone sialoprotein. Although multiple characteristics such as surface topography, chemical composition and mechanical properties differ in the preparations of our collagen-rich milieu, our observations support the notion that geometrical alterations in ECM environments can alter the phosphorylation pattern of p130Cas, FAK, ERK1/2 and p38 MAPK and lead to a differential developmental fate.