The entire immune system develops in the bone marrow from hematopoietic stem cells (HSC) through a set of carefully regulated stages. The earliest stages of differentiation from HSC generate rare cells called lymphoid progenitors, which then in turn produce more mature functional cells of the immune system, the T cells, B cells and NK cells. We have recently discovered methods to identify the earliest lymphoid progenitor stages in normal human bone marrow. In this paper we used this knowledge to explore if lymphoid progenitors are formed normally in the bone marrow of children with certain severe types of genetic immune deficiency (aka severe combine immune deficiency or “bubble baby syndrome”). We found that even though these children cannot produce T cells, they have normal lymphoid progenitors in the bone marrow, demonstrating that their specific genetic mutations block immune cell production after the progenitor stage of development.