ABSTRACT. We investigated gene expression in embryonic stem (ES) cells, induced pluripotent stem (iPS) cells, and fibroblasts. Microarray expression data sets obtained from the Gene Expression Omnibus were analyzed using the Partek software. Human genes from ES cells, iPS cells, and fibroblasts were ranked from low to high according to their expression levels. The gene expression mode in iPS cells was much more like the mode in ES cells, and the expression levels of fibroblast genes fluctuated more dramatically than those of iPS and ES cells. The number of genes with significantly different expression was lower in the iPS and ES cells. Several genes with the expression levels that were significantly different between ES and iPS cells were found, including LEFTY2, DLK1, and NLRP2. Four genes belonged to the low expression category in fibroblasts with the high expression category occurring in ES cells, i.e., HESRG, PROM1, NTS, and LRRN1. Analyzing the expression of these genes is helpful to elucidate the mechanisms of cell fate regulation and efficiently obtain iPS cells.