He did his Pediatrics training at the University of Minnesota, interrupted by a two-year period as a pediatrician in the United States Navy Medical Corps in Portsmouth and Norfolk, Virginia.
In 1960 Sanfilippo was awarded a postdoctoral research fellowship and began a comprehensive study of children with mucopolysaccharide storage disease at the University of Minnesota.
The majority of the heparitin sulfate excreters had a normal or near-normal facial appearance and displayed mild to slight somatic and radiographic manifestations in comparison with their Hunter–Hurler counterparts, who showed more severe involvement.
Sanfilippo presented the results of the study at the annual American Pediatric Society Meeting in May 1963, and published a report later that year.
During his practice years he participated in regional health care planning and published a perinatal mortality review study (1976).