Human exposure to Per- and polyfluoroalkyl substances (PFAS) is ubiquitous and these compounds are some of the most prominent contaminants in humans. The toxicity of perfluorooctane sulfonate (PFOS) and perfluorooctanoate (PFOA) is somewhat known, however data on lesser-understood PFAS are limited. Studies in rodents showed that exposure to PFAS resulted in liver toxicity and liver carcinogenesis. Whether this is also the case in humans it is less clear. Thus we used primary human liver cell spheroids to identify toxic liver effects. New approach methodologies (NAMs) that apply bioinformatic tools to high-throughput data are being increasingly considered to inform risk assessment for data-poor chemicals. In this study we identified biological response potencies (i.e., benchmark concentrations: BMCs) following PFAS exposures to inform read-across for risk assessment of data-poor PFAS. Gene expression changes were measured in the primary human liver cell microtissues (i.e., 3D spheroids) after 1-day and 10-day exposures to increasing concentrations of 23 PFAS. The cells were treated with subgroups of PFAS: carboxylates (PFCAs), sulfonates (PFSAs), fluorotelomers, and sulfonamides. We identified differentially expressed genes and transcriptomic BMCs. Further, we examined phenotypic changes by microscopic imaging. The combined high-throughput transcriptomic and bioinformatic analyses and microscopy support the capability of NAMs to efficiently assess the effects of PFAS in liver microtissues.