Microtubule-associated protein 1B (MAP1B), a member of MAP1 family, plays a key role in the brain development. MAP1B binds to many kinds of proteins directly or indirectly. In our previous studies, MAP1B and glyceraldehydes 3-phosphate dehydrogenase (GAPDH) were down-regulated in bovine follicular cystic follicles (FCF). This study was performed to examine interaction between MAP1B and GAPDH in bovine follicles using immunoprecipitation (IP) with western blot analysis and immunohistochemisty. MAP1B and GAPDH mRNA expression levels were down-regulated in bovine FCFs. Consistent with the semi-quantitative PCR data, their protein expressions were also down-regulated in FCFs. IP data showed that MAP1B bound to GAPDH in normal follicles, but their binding was absent in FCFs, suggesting that these data might be resulted from a low level of MAP1B and/or GAPDH expression. These results suggest that GAPDH does not as always function as a loading control in bovine follicles.