Runx1, one of three mammalian runt-domain transcription factor family proteins, is essential for definitive hematopoiesis. Based on transfection assays, phosphorylation of Runx1 at the three serine residues, Ser249, Ser266, and Ser276, was thought to be important for trans-activation activity of Runx1. By using "knock-in" gene targeting, we generated mouse strains expressing mutant Runx1 protein that harbored a combined serine-to-alanine substitution at either of two residues, Ser249/Ser266 or Ser249/Ser276. Either mutation resulted in a lack of major phosphorylated form of Runx1. However, while loss of definitive hematopoiesis and impaired thymocyte differentiation was observed following the loss of Runx1, these phenotypes were rescued in those mice lacking the major phosphorylated form of Runx1. These results not only challenge the predicted regulation of Runx1 activity by phosphorylation at these serine residues, but also reaffirm the effectiveness of "knock-in" mutagenesis as a powerful tool for addressing the physiological relevance of post-translation modifications.