Transactivation of the expression of metallothionein genes involves the Metal-responsive Transcription Factor (MTF-1). We report here the identification of mtf-1.1a, the first known splice variant of mtf-1.1 mRNA, in common carp (Cyprinus carpio). The lack of a 103 nt internal segment results in a frame shift, causing the early termination of translation. mtf-1.1a mRNA encodes a protein consisting of the first 349 amino acids of MTF-1.1 plus an additional 64 amino acids, with no significant similarity to any of the proteins in the databases. The predicted MTF-1.1a protein carries the Zn-finger domain and the nuclear exporting and nuclear localization signals, and lacks the transcription activation domains. mtf-1.1a was detected in all tissues examined but the liver, with the highest level in the brain. Arsenic alters the levels of both mtf-1.1 and mtf-1.1a transcripts, in an isoform- and tissue-specific manner.