Great range of electrocardiogram (ECG) signal processing methods can be found in the literature. In addition, the importance of gender differences in physiological activities was also identified in various conditions. This article aims to provide a comprehensive evaluation of linear and nonlinear ECG parameters to indicate suitable signal processing approaches which can show significant differences between men and women. These differences were investigated in two conditions: (i) during rest condition, and (ii) during the affective image inducements. A wide range of parameters from time-, frequency-, wavelet-, and nonlinear-techniques were examined. Applying the Wilcoxon rank sum test, significant differences between two genders were inspected. The analysis was performed on 47 college students at rest condition and while subjects watching four types of affective pictures, including sadness, happiness, fear, and peacefulness. The impact of these emotions on the results was also investigated. The results indicated that 72.95% and 72.61% of all features were significantly different between male and female in rest condition and affective inducements, respectively. In addition, the highest percentage of the significant difference between ECG parameters of men and women was achieved using nonlinear characteristics. Considering all features together, the highest significant difference between two genders was achieved for negative emotions, including sadness and fear. In conclusion, the results of this study emphasized the importance of gender role in cardiac responses during rest condition and different emotional states. Since these gender differences are well manifested by nonlinear signal processing techniques, dynamical gender-specific ECG system may improve the automatic emotion recognition accuracies.