The catalase multi-gene family in Arabidopsis includes three genes encoding individual subunits which associate to form at least six isozymes that are readily resolved by non-denaturing gel electrophoresis. CAT1 and CAT3 map to chromosome 1, and CAT2 maps to chromosome 4. The nucleotide and deduced amino acids sequences of the three coding regions are highly related to each other and to other catalases. Both the individual isozymes and the individual subunit mRNAs show distinct patterns of spatial (organ-specific) expression. Six isozymes are detected in flowers and leaves and two are seen in roots. All three mRNAs are highly expressed in inflorescences, and CAT2 and CAT3 are highly expressed in leaves. All three mRNAs are detectable in freshly imbibed seeds, although the pattern of mRNA relative abundance varies among the three genes during early germination. CAT1 and CAT2 mRNA abundance is induced by light. In contrast, CAT3 is negatively light-responsive. CAT2 and CAT3 mRNA abundance is controlled by the circadian clock. Interestingly, the peak in CAT3 mRNA abundance occurs in the subjective evening, which is out of phase with expression of the Arabidopsis CAT2 catalase gene that shows clock-regulated expression gated to the subjective early morning. CAT1 mRNA abundance is not clock-regulated.