This study addresses changes in health which were consequential to the Neolithic transition in the southern Levant, judged on the basis of the study of specific and nonspecific stress indicators, trauma, and degenerative joint disease in 200 Natufian (hunter-gatherer) skeletons (10,500-8300 BC) and 205 Neolithic (agricultural) skeletons (8300-5500 BC) from the southern Levant. The comparison of the health profiles of pre-Neolithic (Natufian) and Neolithic populations reveals a higher prevalence of lesions indicative of infectious diseases among the Neolithic population, and an overall reduction in the prevalence of skull trauma among males. No change over time was observed in the prevalence of degenerative joint disease. These results indicate that in the southern Levant the Neolithic transition did not simply lead to an overall deterioration in health but rather resulted in a complex health profile which was shaped by 1) an increase exposure to disease agents, 2) changes in diet, 3) population aggregation in larger and denser settlements, 4) changes in activity patterns and the division of labor, and possibly 5) a higher resistant immunological system and response capacity to environmental aggressions (mainly infections).