The molecular interactions between transcription factors and cofactors play crucial roles in various biological processes, including haematopoiesis. FOG-1 is a cognate cofactor of GATA-1, and the FOG-1/GATA-1 complex is essential for the haematopoietic differentiation of erythroid cells and megakaryocytes. In order to elucidate the biological functions of FOG-1 in the different contexts of cell differentiation, we analysed the effects of FOG-1 expression on haematopoietic cell differentiation, using a combination of in vitro differentiation of mouse embryonic stem (ES) cells and conditional gene expression. FOG-1 suppressed the proliferation of primitive and definitive erythroid cells in all stages of differentiation. However, FOG-1 inhibited and enhanced megakaryopoiesis in the early and late differentiation stages, respectively, through different molecular mechanisms. In addition, FOG-1 inhibited the proliferation of ES cells, the molecular mechanism of which differs from those of erythroid and megakaryocytic cells. These results suggest that FOG-1 functions in a cell differentiation context-dependent manner.