In an effort to identify possible risk factors for stroke in Sickle Cell Anemia (Hb SS), we analyzed the distribution of alpha-globin gene deletions in a group of Hb SS patients with and without stroke. The group with stroke consisted of 44 patients, (27 male, 17 female) with a mean of 7.5 years at time of stroke. The control group (non-stroke) had 256 Hb SS patients (126 male, 130 female) with a mean age of 7.7 years. There were 9 patients with heterozygous alpha-thalassemia in the stroke group (20.5%). In the control group, there were 93 patients with heterozygous alpha-thalassemia and 5 with homozygous alpha-thalassemia. The incidence of alpha-thalassemia in Hb SS patients without stroke (38%) was comparable to that reported for the African-American population in general. The incidence in the stroke population (20.5%) was significantly lower (P = 0.02) These results indicate that alpha-thalassemia is associated with a lower risk of stroke in Hb SS. This observation should be confirmed in studies involving larger numbers of patients. Possible protective effects of alpha-thalassemia are unknown but may be related to decreased hemolysis and more favorable rheologic properties of red blood cells.