In this study, the effects of electromagnetic fields (EMFs) emitted by GSM900 based mobile phones (MPs) on the heart rate variability (HRV) were examined by using nonlinear analysis methods. The largest Lyapunov exponent (LLE) calculation was used to evaluate the effect of MP under various real exposure conditions. Sixteen healthy young volunteers were exposed to EMFs emitted by GSM900 based MP at two levels from a very low EMF (MP at stand-by) to a higher EMF (MP at pre-ring handshaking and ringing). A blind experimental protocol was designed and utilized with consideration to the physiological and psychological factors that may affect HRV. The results showed that the LLE values increased slightly with higher EMF produced by MP (P < 0.05). This change indicates that the degree of chaos in the HRV signals increased at higher EMF compared to low level EMF. Consequently, we have concluded that high level EMF changed the complexity of cardiac system behavior, significantly.