Background: Beta thalassemia is a disorder that is due to the reduction or lack of production of the beta hemoglobin chain, and its inheritance is in the form of autosomal ressesive. The previous program was the prevention of beta thalassemia from the Eighties in Iran and was accompanied by a significant reduction of birthrate with severe and moderate form of disease, and by improving; the cost-effectiveness of the new program was recently in the executive country. Because the main goal of both programs is reducing birthrate, therefore, it was decided to compare these two programs in terms of affected newborn identification power. Methods: This cross-sectional study was conducted using simple random sampling. Referring to the archive section of Ali-Asghar Children Hospital, the number 72 of patients with thalassemia (36 thalassemia major and 36 thalassemia intermadia) were extracted. In all cases, there was a complete blood count test and hemoglobin electrophoresis for parents of children with the required data including blood markers (RBC, HB, MCV, MCH, HbA2), and age and gender index of parents in the checklist and analyzed statistically by SPSS 20 and SAS 9. 1 softwares. Results: Based on detection type (Thalassemia major or Intermedia) and using new screening protocol and determining the risk of thalassemia, 7. 89% of couples in patients with thalassemia major and 100% of couples were considered in the group of patients with thalassemia. Also, based on the usual protocol of risky group, 6. 96% of couples in patients with thalassemia major and 100% of couples were enrolled in the group of patients with the Intermedia. In addition, 7. 89% were classified for thalassemia major and 100% in Intermedia, without using hemoglobin. Considering the normal ranges of RBC between 4 and 5. 5 for children, the cases of anemia had been reported in 5. 67%. In addition, in terms of normal range of RBC between 4. 7 to 6. 1, the cases of anemia in male and female were estimated to be 5. 37% and 20%, respectively. In addition, RBCs higher than normal ones were 5. 47% and 5. 22% respectively. In other words, in men, only 15% and women 5. 57% were exposed to normal. Conclusion: According to the results that were obtained in this study, the use of primary protocols due to the cheaper and more accurate detection of high risk cases for beta-thalassemia are also preferred. In addition, due to the high prevalence of hematologic disorders, especially anemia in these individuals, the implementation of the Protocol for the elimination of anemia in these individuals is strongly recommended according to the national Protocol.