Genetic selection for disease resistance encoded in the genomes of blue catfish and channel catfish continues to hold the greatest potential for long-term solutions to aquaculture-based disease outbreaks. Progress towards this goal requires the development of genomic resources for catfish, including expressed sequence tags (ESTs). In the context of catfish immune research, ESTs provide a foundation for both research on individual immune-related genes and microarray-based transcriptome analysis following infection. Both approaches are needed to advance our knowledge of teleost immunity and move closer to identification of genetic sources of disease resistance.