This prospective study assessed the prevalence and genetic analysis of alpha.- and beta-thalassemia and sickle cell anemia (SCA) in Southwest Iran. Hematological indices were measured in 17,581 couples living in Khuzestan Province, Southwest Iran. Individuals with mean corpuscular volume <80, mean corpuscular hemoglobin <27, hemoglobin A2 >= 3/5 were considered as beta-thalassemia traits. Prevalence of minor beta-thalassemia, alpha-thalassemia, SCA, iron deficiency anemia, and silent thalassemia were respectively identified in 995 (5.6%), 1169 (6.65%), 1240 (7.05%), 911 (5.18%), and 1134 (6.45%) individuals using a multiplex amplification refractory mutation system, and direct DNA sequencing of globin genes. Three codons IVS-II-1 (G -> A; 26%; n = 13), IVS-II-1 (G -> T; 16%; n = 8), and IVS-I-110 (G -> A; 14%; n = 7) were the most frequent mutants and IVS-II-1 was the most common beta-thalassemia mutation. Also, based on a gap-polymerase chain reaction assay, genotype frequencies of alpha-globin mutations were -alpha(3.7kb) (50%; n = 25), Med/alpha alpha(thal) (12%; n = 6), and -alpha 4.2/alpha alpha (10%; n = 5), which were the most frequent deletion mutants (72% in total). The most common deletion (50%) was -alpha(3.7kb). Our data suggest that the population of Southwest Iran is at high risk of alpha- and beta-thalassemia caused by these deletion mutants and SCA. Our findings will be useful for developing an efficient control program and genetic counseling. (C) 2018 Atlantis Press International B.V.