Molecularly imprinted polymer(MIP) stationary phases against caffeine and against theophylline were prepared. Separation abilities of the phases were investigated by HPLC. The results showed that the theophylline based MIP stationary phase is highly selective to theophylline, and base lined separation of caffeine and theophylline was achieved. However, the caffeine based MIP stationary phase did not possess specific selectivity to the template molecule, caffeine. MIP with specific selectivity to template molecule can only be prepared when interactions between template and monomer go together.