The scalability performance of several critical bioinformatics applications, including BLAST, FASTA, Smith-Waterman, HMMER, Mascot and ICED, was evaluated on AIX 5.1 and SUSE Linux Enterprise Server 8 for IBM eServer pSeries. These applications are either threaded or OpenMP-enabled parallel implementations. The comparison was conducted on the same LPAR of a p690 with 16 CPUs. The results suggested that the scalability of these applications on AIX and Linux are comparable, in general.