Water disinfection byproducts (DBPs) are a class of chemicals that are produced when chemical disinfectants react with organic materials in untreated water. Cytotoxicity and genotoxicity of DBPs have been systematically evaluated to compile a comparative, quantitative database of in vitro mammalian cell toxicity of DBPs. However, one of the most challenging limitations for current DBP cytotoxicity assessment assays is sample availability. Although our current cytotoxicity assay using a 96-well microplate has been designed to reduce sample consumption, further minimization of the size of the test system would allow us to explore various possibilities for point-of-care applications. We have developed a microfluidic device with micro-pillars that shows high uniformity in distribution of cells across all chambers with low cell count. We compare the performance between the 96-well microplate and the microfluidic device by running 72-hour standalone-on-chip cell culture and cytotoxicity analysis experiments, using dimethyl sulfoxide (DMSO) and ethanol as model toxic agents, and bromoacetic acid (BAA) as a representative DBP. The results show close agreement between the two systems. The measured LC₅₀ values for the 96-well microplate and the microfluidic device are 1.54% v/v and 1.27% v/v for DMSO, 1.44% v/v and 2.92% v/v for ethanol, and 17.6 μM and 8.20 μM for BAA, respectively. The micro-pillar microfluidic device offers a great reduction in sample consumption while maintaining the accuracy of the cytotoxicity analyses of water disinfection byproducts.