This study aimed to characterize the molecular spectrum of β-thalassemia (β-thal) mutations and evaluate the services available for prenatal diagnosis (PND) among the Sistani population of Iran. Mutations were analyzed with amplification refractory mutation system (ARMS), gap-polymerase chain reaction (gap-PCR), multiplex ligation-dependent probe amplification (MLPA) analysis and direct sequencing. Fetal diagnosis was also confirmed by linkage analysis. Over a 9-year period (2002-2011), 405 at-risk Sistani couples were referred for mutation analysis and/or PND. Of the referred couples, 18.5% had one to three affected children with β-thal major (β-TM) and the remainder had no children or were not married. Most of the couples (73.3%) lived in urban areas and the rate of consanguineous marriage was 76.8%. Twenty-one mutations were identified, of which the most frequent ones were IVS-I-5 (G>C) with a frequency of 74.1%, followed by codon 15 G>A (5.0%), codon -88 (C>T) (3.8%), IVS-II-1 (G>A) (3.4%), codons 8/9 (+G) (2.9%) and IVS-I-1 (G>T) (2.7%), which accounted for about 91.9% of the total β-thal mutations for this region. Furthermore, fetal DNA was obtained from chorionic villus sampling (CVS) for 266 pregnant women and 68 (25.5%) fetuses were diagnosed as affected. In summary, β-thal mutations are very heterogeneous and significantly different from those found in other parts of Iran and are similar to those of Pakistani and Indian populations. These results could greatly facilitate timely and accurate PND.