Three-dimensional culture systems such as cell-laden hydrogels are superior to standard 2-D monolayer cultures for many drug-screening applications. However, their adoption in high throughput screening (HTS) have been lagging, in part due to the difficulty of incorporating these culture formats into existing robotic liquid handling and imaging infrastructures. Dispensing cell-laden pre-polymer solutions into 2-D well-plates is a potential solution, but typically requires large volumes of reagents to avoid evaporation during polymerization, which increases cost, makes drug penetration variable and imaging complex. Here we describe a technique to efficiently produce 3-D ‘microgels’ using automated liquid handling systems and standard, non-patterned, flat-bottomed, 384-well plates. Sub-millimeter-diameter, cell-laden collagen gels are deposited on the bottom of ~2.5 mm-diameter microwell with no concerns over evaporation and meniscus effects at the edges of wells, using aqueous two-phase system patterning. The microscale cell-laden collagen-gel constructs are readily imaged and readily penetrated by drugs. Cytotoxicity of chemotherapeutics were monitored by bioluminescence and demonstrates that 3-D cultures confer chemoresistance, as compared to similar 2-D culture. This data hence, demonstrates the importance of culturing cells in 3-D to obtain realistic cellular responses. Overall, this system provided a simple and inexpensive method for integrating 3-D culture capability into existing HTS infrastructure.