Factor IX (FIX) is a component protein of blood coagulation pathway, which activates factor X through interaction with factor VIII and Ca(2+). Defective FIX protein resulting from mutation in the corresponding gene causes an X-linked bleeding disorder known as haemophilia B. The aim of the present study was to speculate the potential detrimental effects of the FIX mutations upon the functionality of the protein, which could contribute to the comprehension of the mechanism underlying haemophilia B. In this report, we examined the effect of point mutation on the crystal structure of the native factor IX by measuring the change in the hydrogen-bonding pattern and electrostatic potential and explored the possibility of any correlation of the clinical severity of haemophilia B with the structural perturbation, by plotting the mutations of varying phenotype (severe and mild) on the crystal structure of FIX. Out of a total of 16 severe mutations 14 (88%) showed changes of hydrogen-bonding pattern to variable extent. Among the nine mild haemophilia B mutations, six (i.e. 66.66%) showed no change in hydrogen-bonding pattern. Our data suggest that there is a statistically significant correlation between the two groups of mutations as measured by change in the hydrogen-bonding pattern. Our study truly represents an initiation of an effort that would provide a framework for first evaluation of suspected mutations by in silico approaches, which might be further validated by other experimental techniques.