Pregnant women with iron deficiency and those who are carriers of haemoglobinopathies present with anaemia of varying severity. There is no antenatal screening for haemoglobinopathies in India. The objective of this study was to determine the prevalence of undiagnosed haemoglobinopathy carriers in a random sample of pregnant women attending antenatal care clinics in Pune city, India. Biobanked DNA of 360 randomly selected pregnant women was genotyped for six common mutations and two common haemoglobin variants, HbS and HbE. Odds ratios (OR) with 95% confidence intervals were computed to determine association of carrier status with socio-demographic, haematological and clinical characteristics. The prevalence of undiagnosed haemoglobinopathy carriers was 6.3% (95% CI 4.2-9.4%) of which 3.3% (95% CI 1.9-5.7%) were beta thalassaemia carriers. There was an increased odds that beta thalassaemia carriers had moderate anaemia (OR 10.59,). This study reveals the high prevalence of undiagnosed haemoglobinopathy carriers among pregnant women, indicating the need to immediately implement carrier screening and genetic counselling services across the country.