INTRODUCTION: The study describes the hospitalization rates and medical diagnoses of children with fetal alcohol syndrome (FAS) and incomplete FAS. METHODS: Two retrospective case-control studies were conducted of Northern Plains American Indian children with FAS or incomplete FAS identified from 1981-93 by using the ICD-9-CM code 760.71. Children who had FAS or incomplete FAS were compared to each other and to children who did not have FAS. RESULTS: Compared to the controls, the 43 children with FAS (Study 1) and 35 children with incomplete FAS (Study 2) were hospitalized more often with otitis media (51.2 percent OR=4.32 and 31.4 percent OR=3.02 respectively), pneumonia (46.5 percent OR=4.21 and 34.3 percent OR=2.54), fetal alcohol syndrome (32.6 percent p=.001 and 14.3 percent p=.007), dehydration (23.3 percent OR=9.29 and 17.1 percent OR=4), and anemia (11.6 percent OR=10 and 17.1 percent p=.002) respectively. Children with FAS were hospitalized more often with failure to thrive (32.6 percent p=.001) and neglect (23.3 percent OR=10.0) than children with incomplete FAS and controls. Children with FAS were hospitalized with child sexual abuse (11.6 percent OR=10.0) and feeding problems (11.6 percent p=.007), and children with incomplete FAS were hospitalized with gastroenteritis (22.9 percent OR=14.55) and bronchitis (22.9 percent OR=3.0) more than control children. CONCLUSIONS: Children with FAS or incomplete FAS had more hospitalizations and longer average length of stays than control children.