Chemical bonding states of doped impurities, boron (B) and arsenic (As), in silicon (Si) shallow junctions were studied by soft X-ray photoelectron spectroscopy (SXPES). A step-by-step shallow etching and Hall effect measurements were combined with the SXPES to investigate correlation between chemical bonding state and electrical activation of the impurities, and to clarify depth profiles of concentration of activated and deactivated impurities in shallow junctions. The study of B doped layer revealed that one chemical bonding state having the lowest biding energy is assigned to activated B and the other two states are correlated with deactivated B, which probably form B clusters. On the other hand, two different chemical bonding states were detected for As. It was found that the state having higher binding energy was correlated with activated As, while another state was probably correlated with deactivated As cluster.