A calcium binding protein of Mr 29,000 which cross-reacts with antibodies raised against chick calbindin-D28k was previously reported to be present in rat cerebellum [Pochet, R., Parmentier, M., Lawson, D. E. M., & Pasteels, J. L. (1985) Brain Res. 345, 251-254]. It was suggested that the Mr 29,000 protein represents another form of calbindin-D28k. In our laboratory we were able to identify Mr 28,000 and 29,000 proteins in rat, human, and chick cerebellum by their ability to bind 45Ca in a 45Ca blot assay. Two calcium binding proteins of Mr 27,680 and 29,450 were isolated from rat cerebelli by the use of gel permeation chromatography and preparative gel electrophoresis. After reverse-phase high-performance liquid chromatography (HPLC) the proteins were sequenced. Sequence analysis by tandem mass spectrometry indicated only 52% identity between the rat cerebellar Mr 28,000 and 29,000 proteins. Thus they are not different forms of the same protein, as previously suggested. Eighty-nine percent identity was observed between the rate cerebellar Mr 29,000 protein and chick calretinin [Rogers, J. H. (1987) J. Cell Biol. 105, 1343-1353]. The difference in identity between the rat cerebellar Mr 29,000 protein and chick calretinin may be due to species differences, and thus this protein is most likely rat calretinin. However, barely detectable levels of mRNA and weak immunoreactivity have been reported for calretinin in cerebellum. Since we found the Mr 29,000 calcium binding protein to be an abundant protein in rat cerebellum, these results suggest either posttranscriptional regulation of calretinin in cerebellum or species differences.(ABSTRACT TRUNCATED AT 250 WORDS)