The present invention relates to a method for selecting induced pluripotent stem (iPS) cells. More particularly, the present invention provides: a method for selecting an iPS cell, comprising the steps of: (1a) measuring the expression level of an exogenous nuclear reprogramming gene(s) in a test iPS cell; and (2a) selecting an iPS cell in which the expression level(s) of an exogenous nuclear reprogramming gene(s) is/are less than or equal to the expression level(s) in control iPS cells; and a method for selecting an iPS cell, comprising the steps of: (1b) measuring the expression level of an exogenous nuclear reprogramming gene(s) and the sum the expression levels of the exogenous nuclear reprogramming gene(s) and the corresponding endogenous gene iPS cell; and (2b) selecting an iPS cell in which the ratio of the expression level of an exogenous nuclear reprogramming gene(s) relative to the sum of the expression levels of the exogenous transgene(s) and the corresponding endogenous gene(s) is less than 1 to the ratio in the control iPS cell.