Multiple intestinal atresias (MIA) is a severe form of intestinal atresias throughout the gastrointestinal tract. In two reports, MIA have been associated with severe immunodeficiency. We report a newborn girl who had profound humoral and B cell immunodeficiency and impaired T cell function. The patient had agammaglobulinemia and decreased blood lymphocytes, with virtually no B cells in the blood or in intestinal lymph nodes. T cells were reduced in number and weakly proliferated to mitogens. These data suggest that a syndrome involving the development of MIA is associated with various forms of severe immunodeficiency, and therefore newborns with MIA should be examined for immunodeficiency.