We investigated molecular crowding effects on the thermodynamic stability of Hoogsteen and Watson-Crick base pairs in an intramolecular duplex and triplex. The melting temperature (Tm) of Hoogsteen base pair formations in the triplex and the duplex increased 3.7 degrees C and 3.2 degrees C, respectively, by adding 20 wt% PEG 200. On the other hand, the Tm of Watson-Crick base pair formations in the triplex and the duplex decreased 5.7 degrees C and 5.2 degrees C, respectively. These results suggested that molecular crowding conditions generally stabilized and destabilized Hoogsteen and Watson-Crick base pairs, respectively, even in the different DNA structures.