This prospective study assessed the prevalence and genetic analysis of
α
- and
β
-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
β
-thalassemia traits. Prevalence of minor
β
-thalassemia,
α
-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-I-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
β
-thalassemia mutation. Also, based on a gap-polymerase chain reaction assay, genotype frequencies of
α
-globin mutations were −
α
3.7 kb
(50%;
n
= 25), Med/
αα
thal
(12%;
n
= 6), and −
α
4.2/
αα
(10%;
n
= 5), which were the most frequent deletion mutants (72% in total). The most common deletion (50%) was −
α
3.7 kb
. Our data suggest that the population of Southwest Iran is at high risk of
α
- and
β
-thalassemia caused by these deletion mutants and SCA. Our findings will be useful for developing an efficient control program and genetic counseling.