Human embryonic stem cells (hESC) are difficult to adapt to 96-well plate assays, such as the MTT assay, because they survive best when plated as colonies, which are not easily counted and plated accurately. Two methods were developed to address this problem. In the first, ROCK inhibitor (ROCKi) was used, which allows accurate counting and plating of single hESC. In the second, small colonies were plated without ROCKi but with adaptations for accurate counting and plating. The MTT assay was also adapted for use with mouse neural stem cells. These methods allow the MTT assay to be conducted rapidly and accurately with high reproducibility between replicate experiments. When screening volatile chemicals in a 96-well plate, vapor effects may occur and dose ranges must be carefully defined. The methods were validated using the NIH assay guidance tool. These methodss could readily be translated to other 96-well plate assay.