This study was undertaken to determine the prevalence and molecular basis of alpha-thalassemia in the Indian population and its implications in genetic counseling and prenatal diagnosis. 1253 random samples were screened for hemoglobinopathies. Red cell indices were measured on the Sysmex K 1000 cell counter; HbA2 and HbF levels were quantitated using high performance liquid chromotography (HPLC). Cellulose acetate electrophoresis and isoelectric focusing (IEF) was done to detect the presence of Hb Bart's in cord blood samples. alpha-Globin gene mapping was done using Southern blot hybridization of BamHI and BglII digests. Of the 1253 subjects, 132 had a single alpha-gene deletion (10.5%) while 29 had two alpha-gene deletions (2.31%). Fifteen cases showed the presence of alpha-gene triplication (1.1%). A single case showed the presence of one alpha-gene deletion as well as alpha-gene triplication (-alpha/alphaalphaalpha). Overall, the prevalence of alpha-thalassemia was 12.9%. Region-wise and caste-wise analysis showed the highest prevalence of alpha-thalassemia among the Punjabi population originating from the northern region of India. alpha-Thalassemia is by far the commonest hemoglobinopathy in India, but it is not a cause of serious genetic risk is the milder form (-alpha/alphaalpha) of alpha-thalassemia, which is predominant. Knowing the alpha-genotype is useful for genetic counseling for prenatal diagnosis in couples where one of the parents may have reduced indices coupled with a raised RBC count and normal HbA2 levels.