In the present research, we evaluated the health effects of exposure to the municipal waste incinerator (MWI) in Pisa, Italy, through a population-based cohort design. The individual exposure pattern in the area was estimated through CALPUFF dispersion models of NOχ (developed by Atmospheric Studies Group Earth Tech, Lowell, Massachusetts), used as pollution proxies of the MWI and the relevant industrial plant, and through land-use regression for NOχ due to traffic pollution. Using Cox regression analysis, hazard ratios (HR) were estimated adjusting for exposure to other sources of pollution, age, and socioeconomic deprivation. An adjusted linear trend of HR (HRt) over the categories of exposure, with the relative 95% CI and p-value, was also calculated. Mortality and hospital discharge were studied as impact outcomes. Mortality analysis on males showed increased trends of mortality due to natural causes (HRt p < 0.05), the tumor of the lymphohematopoietic system (HRt p = 0.01), cardiovascular diseases (HRt p < 0.01); in females, increased trends for acute respiratory diseases (HRt p = 0.04). Morbidity analysis showed a HRt for lymphohematopoietic system tumor in males (HRt p = 0.04). Some of the excesses are in agreement with previous evidence on the health effects of MWIs, although the observation in males but not in females, suggests a cautious interpretation. Confounding due to other sources of exposure cannot be ruled out. The evidence was considered important in the decision-making process of the waste cycle.