The non-structural protein 1 (NS1) of the influenza A virus and the protein NS2, which is also known as nuclear export protein, play important roles in the infectious life cycle of the virus. The objective of this study was to find the degree of conservation in the NS proteins and to identify conserved sites of functional or structural importance, which may be utilised as potential drug target sites. The analysis was based on 2620 amino acid sequences for the NS1 protein and 1195 sequences for the NS2 protein. The degree of conservation and potential binding sites were mapped onto the protein structures obtained from a combination of experimentally available structure fragments with predicted threading models. In addition to high conservation in protein regions of known function, novel highly conserved sites have been identified, namely Glu159, Thr171, Val192, Arg200, Glu208 and Gln218 on the NS1 protein and Ser24, Leu28, Arg66, Arg84, Ser93, Ile97, and Leu103 on the NS2 protein. Using the Q-SiteFinder binding site prediction algorithm, several highly conserved binding sites were found including two spatially close sites on the NS1 protein, which could be targeted with a bivalent ligand that would interfere with double-stranded RNA binding. Altogether, this work reveals novel universally conserved residues that are candidates for protein-protein interactions and provide the basis for designing universal anti-influenza drugs.