With the success of human genome project, a large number of predicted genes were sequenced, requiring functional assays for their characterization in a high-throughput manner. To identify novel human genes associated with cell apoptosis, a high-throughput assay was established. Candidate sequences were amplified and cloned in pcDNA3.1/myc-His(-)B, then were transfected into HeLa cells respectively. The expression vector encoding BAX was used as the positive control, which was wildly-known to effectively induce programmed cell death. JC-1 staining was utilized to assess the mitochondrial membrane potential, which could collapse in the early stage of apoptosis. 600 human novel genes were screened and seven positive genes (CHMP6, CGI-38, hCAP-H2, NUDT16L1, ARMC1, PHF17, and FLJ21103) were found out. A subsequent validation by flow cytometry revealed that three of the seven genes (CHMP6, CGI-38, hCAP-H2) were with functions related to cell apoptosis. In HeLa cells transfected with the above three expression vectors, the proportion of single annexin-V-positive cells was evidently increased (8.01%, 6.88%, 5.01%) compared with PCDB-transfected cells (3.43%). Bioinformatics analysis of the three positive genes reveals that their functions are known little and the relationships between the three genes and cell apoptosis have not previously been reported. These results therefore indicate that a rapid and effective screening system has been studied. Further studies will perform on the 3 genes associated with cell apoptosis.