The comparison of differentiated induced pluripotent stem cells (iPSCs) derived from patients with disease to differentiated iPSCs derived from healthy patients enables powerful disease modeling. By performing an informal retrospective survey of disease modeling studies published in high impact journals, we found that the median and average number of controls used in these studies were 1 and 1.6, respectively. The bulk of these studies did not control for age, gender and ethnicity. Since a large proportion of phenotypic differences observed between iPSC lines are due to genetic variation or variation between lines, this is an insufficient number of controls to confidently rule out standard variation. Future studies need to include more controls and ensure that these controls are appropriately matched for gender, age and ethnicity.