Haemoglobinopathies are a leading cause of child mortality worldwide, although with a variable geographical incidence. A reliable estimate of prevalence of the disease is necessary for reducing its burden. However, most studies in India are either hospital based or from certain regions of the country and hence may not realistically reflect the disease burden. The eastern Indian states of Bihar, Chhattisgarh and Jharkhand and eastern region of Uttar Pradesh, which comprise ~25 % population of the country, are poorly studied with respect to haemoglobinopathies. The present study, conducted on 1,642 individuals from this region, shows a frequency of 3.4 % for β-thalassaemia trait (BTT), 3.4 % for sickle cell haemoglobin trait (HbS)/haemoglobin E trait (HbE) and 18 % for α-globin defects. While BTT mutations are distributed rather uniformly across the region, HbS occurs only in Chhattisgarh and Jharkhand, the regions rich in tribal populations. The frequency of α-gene mutation is strikingly high, occurring even in individuals with normal blood count, in tribal as well as non-tribal groups. The mutation spectrum of BTT is also distinct since the common mutations, IVS1-1 (G-T) and 619 bp del, are absent while CD15 (G-A) is the second most frequent. The HbA2 level in the suspected cases is strikingly low. We demonstrate association of the low HbA2 level with vitamin B12 and folate deficiency in this cohort. Thus, the present report besides providing an estimate of the carrier frequency of β-thalassaemia traits also confirms high prevalence of α-gene defects and regional heterogeneity in distribution of HbS in the eastern parts of India.