It is estimated that in the world there are between 6 and 7 million people infected with Chagas disease, mainly in endemic areas of 21 Latin American countries, and in recent years it is slowly becoming a health problem in more urban areas and countries. In that sense, developing diagnosis methods is primordial. That is why this work used a deep neural network to classify 292 subjects (volunteers and patients) composed of 83 health volunteers (Control group); 102 asymptomatic chagasic patients (CH1 group) and 107 seropositive chagasic patients with incipient heart disease (CH2 group). Approximate Entropy ApEn was calculated from the tachograms of the circadian profiles of 24 hours every 5 minutes (288 frames) of each subject, and part of this data were used to train the network. The classification work done by the deep neural network had 95% of accuracy and 95% of precision, validated with the ROC curve, whose AUC values were 0.98 for control group, 0.99 for CH1 group and 0.98 for CH2 group. Taking into account the good performance, we can consider this deep neural network and approximate entropy as useful tools to have a good early diagnosis about Chagas disease and its cardiac compromise.