Bayesian Analysis of Gene Expression Levels (BAGEL) is a program that allows statistical inferences to be made regarding differential gene expression between two or more samples measured on spotted (two-channel) microarrays. BAGEL makes these inferences from normalized ratio data, on a gene-by-gene basis. The advantages of BAGEL include ease of use, straightforward interpretation of results, statistical robustness, flexibility in accepting different experimental designs, and that it is free. BAGEL was written by Jeffrey Townsend, who periodically updates and improves the program, and to whom bugs should be reported. BAGEL is available for Windows, Mac OS9, Mac OSX, and Linux.