Primary Immune Defects (PID) are a group of congenital disorders based on mutations of molecules essential for normal immunity. To investigate the perceived prevalence of various PIDs in New York State, we used the Statewide Planning and Research Cooperative System (SPARCS) data to identify hospitalized subjects with any of a group of ICD diagnosis codes applied from 2000 to 2004. Amongst 13,539,358 hospitalizations of 4,777,295 patients, we found 2,361 patients (0.05% of the admitted patients) diagnosed with one or more PID codes. As a group, these patients were younger, had more admissions and stayed in the hospital longer than other patients. They were more likely to be Caucasian non-Hispanic, non African American, less likely to have Medicare, and more likely to have Medicaid or Blue Cross insurance than other inpatients. Most patients resided in the most populous counties, Kings, New York and Queens Counties, but the distribution of the patients’ home zip codes was not proportional to county populations, suggesting lack of recognition of immune defects in some locations. Antibody defects were the commonest diagnoses made. There were 143 cases of severe combined immune deficiency (SCID) and 30 cases of Wiskott Aldrich syndrome (WAS), diagnoses most likely to lead to a hospitalization. The estimated prevalence of these defects in this population would be 1 in 136,363.6 and 1 in 650,000 persons, significantly less than the predicted overall incidence which is 1 in 50,000 to 1 in 100,000 for SCID and 1 in 250,000 for WAS. The hospital charges, over five years, for the subjects with SCID was $36,414,220.70, for an average of $254,645 per patient.