Regeneration of functioning tissue essentially involves recapitulating relevant aspects of organogenesis, so that the starting composite of cells, matrix, and molecular factors develops into the desired structure and physiology. A crucial aspect of development is local cell—cell communication; that is, molecular regulatory factors are more typically paracrine and autocrine than endocrine in nature. Autocrine loops were originally thought of predominantly as being involved in pathological behavior, but it is becoming increasingly clear that a large portion of normal physiological behavior—and a tremendous portion of development—is strongly regulated by autocrine factors (1). Thus, continuing progress of the field of tissue engineering will require increased understanding of how autocrine loops operate, so that they can be designed or manipulated systematically. We have made an effort in this direction, and some early experimental and modeling results can be found in the literature (2–5). In this chapter, we describe the methods we have used for creating autocrine cell loops and quantitatively assessing their operation.