Fragmentation of imidazole, pyrimidine and purine into pairs of cations induced by carbon 1s core ionization was studied. All three molecules favor two-body fragmentation accompanied with a number of hydrogen ejections. In addition, also the formation of CH1,2N+ strongly characterizes the fragmentation of imidazole, pyrimidine and purine. As purine is a fusion of imidazole and pyrimidine rings, the measurements carried out also provided a possibility to study how the fragmentation changes when an isolated imidazole or pyrimidine molecule becomes a part of a larger structure. Furthermore, the previous studies on two pyrimidine derivatives, thymine and uracil, also provide an opportunity to see how the attachment of simple functional groups affect the fragmentation of pyrimidine. The results suggest that the fragmentation of pyrimidine is rather sensitive to any structural or environmental changes, unlike the fragmentation of imidazole.