Induced pluripotent stem cells (iPSCs) are rapidly evolving into an important research tool due to their close resemblance with pluripotent embryonic stem cells (ESCs). Of particular interest at this point are iPSC applications in disease modeling and drug discovery/testing. The high mobility group AT-hook 2 (HMGA2) protein is a nonhistone chromatin factor normally expressed in ESCs and during early developmental stages. Aberrant HMGA2 expression is associated, for example, with abnormal body stature, diabetes mellitus, heart development and uterine leiomyomas. Furthermore, the protein is re-expressed in many primary tumor cells and plays an important role in metastasis. Here we used iPSC formation in conjunction with exogenous human HMGA2 expression to gain insight into biological functions of HMGA2. Gene expression profiling and gene ontology analyses showed that anatomical development and cell adhesion/differentiation processes are strongly affected by HMGA2. This could help to uncover, at the molecular level, some of the known phenotypic consequences of aberrant HMGA2 expression. Furthermore, our data showed that expression of key diabetes susceptibility genes is influenced by HMGA2, which revealed an interesting link to the recently indentified Lin28/let-7 pathway regulating mammalian glucose metabolism. Contrary to a previous report, our results indicate that HMGA2 is not involved in the regulation of telomerase gene expression. Finally, our data support a model in which tight regulation of intracellular HMGA2 levels is important both to maintain a pluripotent ESC state and to induce differentiation into certain cell lineages during later developmental stages.