Background: With a possible increased risk of iron absorption for those with thalassemia, many clinicians hesitate to adopt a universal iron supplementation program for all infants. Therefore, we aimed to determine thalassemia prevalence in 6 to 12-month old infants, along with the iron status of those with and without thalassemia. Procedures: We performed a cross-sectional descriptive study of healthy infants attending the Well Baby Clinic at Thammasat University Hospital. All enrolled were evaluated for complete blood count, hemoglobin electrophoresis, iron parameters, and molecular genetics for common α- and β-thalassemia. Results: Overall, 97 of 206 (47%) participants had thalassemia minor, Hb E traits being the majority; none had thalassemia intermedia or major. Familial history of anemia or thalassemia was an increased risk for detecting thalassemia minor in offspring (OR 5.18; 95% CI 2.60-10.33, P=0.001). Between normal and iron-replete thalassemia minor infants, there were no statistical differences in transferrin saturation, serum ferritin, and hepcidin. However, one-third of those with thalassemia minor (31/97) also had iron deficiency anemia (IDA) with a similar risk of having iron deficiency to infants without thalassemia. There was no hepcidin suppression in our infants with thalassemia minor compared to healthy controls. Conclusions: In Southeast Asia, thalassemia and IDA are endemic, and infants with thalassemia minor, particularly Hb E and β-thalassemia trait, are also at risk of IDA; thus, our short-term universal iron supplementation program for 6 to 12-month old infants should not increase the risk of those with thalassemia minor developing iron overload in the future.