Mutations in Factor IX gene (F9) cause X-linked recessive bleeding disorder hemophilia B. Here, we characterized molecular events in nine North Indian hemophiliac families identifying four missense mutations (three novel), two nonsense mutations, and a deletion. We have also captured the mutational spectrum of this disease in India based on available reports and established their genotype/phenotype relationships. Indian F9 mutations data indicate the absence of an important germline mutagen in the Indian subcontinent over the last century, and are consistent with previously made conclusions that universal, presumably endogenous factors are predominant in the causation of the spontaneous mutations in F9. We also analyzed the distribution of Ala194Thr polymorphism in 1231 Asian Indians and have established that Ala variant is far more frequent and can certainly be exploited for carrier detection, contrary to earlier reports.