Density functional theory (DFT) was utilized to study intermolecular interactions between caffeine (CAF) and cytarabine (CYT) using B3LYP, PBEKCIS and MPWPW91 methods. Also, the mentioned interactions were investigated using MP2 method. Effects of various factors on stability of the most stable conformers of binary complex CAF-CYT were examined. Results indicate that competition between hydrogen bond and CH…N bond interactions influences the binding energy values of the conformers of binary complex CAF-CYT. Indeed, results of electronic charge densities, population analyses and charge transfer studies were considered. CAF is the analogue base of adenine (A) and may pair with thymine (T) to form CAF-T instead of A-T base pair and so has mutagenic effects. It seems that the intermolecular interactions between CAF and CYT play an interference role on mutagenic effects of this molecule. A new aspect was proposed for CYT in addition to traditional anti-cancer quality of this drug.