Gradients of molecular signaling factors play an essential role in numerous events in embryonic development, from patterning limb and organ formation to the intricate shaping of the brain and neuroanatomical architecture. These gradients are a consequence of diffusion dynamics in tissues, and newly published work describes two vital aspects of these diffusion processes in tissue development—first, the influence of molecular diffusion gradients on stem cell signaling pathways is described in detail, including a summary of recent discoveries in how gas and nutrient concentrations can influence stem cell potency, differentiation, and metabolism. Secondly, the paper describes novel applications of diffusion equations to model concentration gradients of nutrients and signaling factors in three-dimensional (3D) tissue constructs under a variety of conditions, including with or without cellular metabolism of the diffusing substance.