Background The aim of the study was to examine the differences of boredom, pain, and surprise. In addition to that, it was conducted to propose approaches for emotion recognition based on physiological signals. Methods Three emotions, boredom, pain, and surprise, are induced through the presentation of emotional stimuli and electrocardiography (ECG), electrodermal activity (EDA), skin temperature (SKT), and photoplethysmography (PPG) as physiological signals are measured to collect a dataset from 217 participants when experiencing the emotions. Twenty-seven physiological features are extracted from the signals to classify the three emotions. The discriminant function analysis (DFA) as a statistical method, and five machine learning algorithms (linear discriminant analysis (LDA), classification and regression trees (CART), self-organizing map (SOM), Naïve Bayes algorithm, and support vector machine (SVM)) are used for classifying the emotions. Results The result shows that the difference of physiological responses among emotions is significant in heart rate (HR), skin conductance level (SCL), skin conductance response (SCR), mean skin temperature (meanSKT), blood volume pulse (BVP), and pulse transit time (PTT), and the highest recognition accuracy of 84.7 % is obtained by using DFA. Conclusions This study demonstrates the differences of boredom, pain, and surprise and the best emotion recognizer for the classification of the three emotions by using physiological signals.