Channel catfish (Ictalurus punctatus) is the predominant aquaculture species in the United States. Its production suffers severe losses due to frequent outbreaks of diseases. The major disease problems are bacterial diseases including enteric septicemia of catfish (ESC) and columnaris disease. ESC disease has been worked for years and a good understanding of host responses has been achieved. However, little work has been conducted on columnaris disease, particularly so with understanding of the host mucosal immune responses at sites of attachment and infection, e.g., the gill. In this work, we conducted RNA-Seq using Illumina sequencing with RNAs isolated from the gill tissue of both healthy and infected catfish at various times after challenge. A total of approximately 203.2 million paired reads were obtained. They were assembled into contigs by de novo assembly. Using a two-fold cut-off, analysis of the digital counts of expressed genes allowed identification of 1,972 differentially expressed genes, of which nearly two-thirds were up-regulated and about one third were down-regulated. Quantitative real-time PCR assays are being conducted to validate the RNA-Seq data, and gene ontology enrichment analysis and pathway analysis are also being conducted to gain understanding of the overall molecular responses of the host against columnaris infection. This work represents the first comprehensive analysis of host gene expression after infection with columnaris. Such molecular information should provide a reference set of significantly regulated immune-related genes for future studies, and provide some insight as to selection strategies for the development of resistance catfish brood stocks in aquaculture.