Described here is a simple, high-throughput process to fabricate pellets with regular size and shape and the assembly of pre-cultured pellets in a controlled manner into specifically designed 3D plotted porous scaffolds. Culture of cartilage pellets is a well-established process for inducing re-differentiation in expanded chondrocytes. Commonly adopted pellet culture methods using conical tubes are inconvenient, time-consuming and space-intensive. We compared the conventional 15-mL tube pellet culture method with 96-well plate-based methods, examining two different well geometries (round- and v-bottom plates). The high-throughput production method was then used to demonstrate guided placement of pellets within a scaffold of defined pore size and geometry for the 3D assembly of tissue engineered cartilage constructs. While minor differences were observed in tissue quality and size, the chondrogenic re-differentiation capacity of human chondrocytes, as assessed by GAG/DNA, collagen type I and II immunohistochemistry and collagen type I, II and aggrecan mRNA expression, was maintained in the 96-well plate format and pellets of regular size and spheroidal shape were produced. This allowed for simple production of large numbers of reproducible tissue spheroids. Furthermore, the pellet-assembly method successfully allowed fluorescently labelled pellets to be individually visualised in 3D. During subsequent culture of 3D assembled tissue engineered constructs in vitro, pellets fused to form a coherent tissue, promoting chondrogenic differentiation and GAG accumulation.