Several cases that do not fit the agricultural adaptation model, in which people's health deteriorated with the shift from hunting-gathering to farming, have been reported, such as the introduction of rice agriculture during the Yayoi Period in Japan and the Iron Age in Southeast Asia, where health was maintained or improved. However, the health of rice farmers in the homeland areas has rarely been reported. This study aims to clarify the frequency and degree of stress markers inscribed on Neolithic human bones in the Yangtze River Delta, one of the origins of rice agriculture, and to elucidate the state of adaptation when humans first engaged in rice agriculture. The materials of this study are the Early Neolithic site of Majiabang, and the Late Neolithic sites of Guangfulin and Jiangzhuang. Several millet farming groups in northern China were used as comparative materials. The results show that the Neolithic rice farming groups in the Yangtze River Delta generally had a higher frequency of stress markers than the millet farming groups in northern China. In particular, the Late Neolithic Guangfulin assemblage had higher frequencies, while the Early Neolithic Majiabang assemblage tended to have relatively low frequencies of porotic hyperostosis and cribra orbitalia. These results suggest that people's health deteriorated in the Late Neolithic period, when the scale of paddy rice cultivation expanded, as a result of the new subsistence activities and rice-oriented diet.