This paper reviews the technologies that have been invented in the last few years on high-throughput phenotyping, imaging, screening, and related techniques using microfluidics. The review focuses on the technical challenges and how microfluidics can help to solve these existing problems, specifically discussing the applications of microfluidics to multicellular model organisms. The challenges facing this field include handling multicellular organisms in an efficient manner, controlling the microenvironment and precise manipulation of the local conditions to allow the phenotyping, screening, and imaging of the small animals. Not only does microfluidics have the proper length scale for manipulating these biological entities, but automation has also been demonstrated with these systems, and more importantly the ability to deliver stimuli or alter biophysical/biochemical conditions to the biological entities with good spatial and temporal controls. In addition, integration with and interfacing to other hardware/software allows quantitative approaches. We include several successful examples of microfluidics solving these high-throughput problems. The paper also highlights other applications that can be developed in the future.