The Wnt and the bone morphogenic protein (BMP) pathways are evolutionarily conserved and essentially independent signaling mechanisms, which, however, often regulate similar biological processes. Wnt and BMP signaling are functionally integrated in many biological processes, such as embryonic patterning in Drosophila and vertebrates, formation of kidney, limb, teeth and bones, maintenance of stem cells, and cancer progression. Detailed inspection of regulation in these and other tissues reveals that Wnt and BMP signaling are functionally integrated in four fundamentally different ways. The molecular mechanism evolved to mediate this integration can also be summarized in four different ways. However, a fundamental aspect of functional and mechanistic interaction between these pathways relies on tissue‐specific mechanisms, which are often not conserved and cannot be extrapolated to other tissues. Integration of the two pathways contributes toward the sophisticated means necessary for creating the complexity of our bodies and the reliable and healthy function of its tissues and organs. Developmental Dynamics 239:16–33, 2010. © 2009 Wiley‐Liss, Inc.