Pesticides are extensively used by farmers in China. However, the effects of pesticides on farmers' health have not yet been systematically studied. This study evaluated the effects of pesticides exposure on hematological and neurological indicators over 3 years and 10 days respectively. A cohort of 246 farmers was randomly selected from 3 provinces (Guangdong, Jiangxi, and Hebei) in China. Two rounds of health investigations, including blood tests and neurological examinations, were conducted by medical doctors before and after the crop season in 2012. The data on pesticide use in 2009-2011 were collected retrospectively via face-to-face interviews and the 2012 data were collected from personal records maintained by participants prospectively. Ordinary least square (OLS), Probit, and fixed effect models were used to evaluate the relationship between pesticides exposure frequency and the health indicators. Long-term pesticide exposure was found to be associated with increased abnormality of nerve conductions, especially in sensory nerves. It also affected a wide spectrum of health indicators based on blood tests and decreased the tibial nerve compound muscle action potential amplitudes. Short-term health effects included alterations in complete blood count, hepatic and renal functions, and nerve conduction velocities and amplitudes. However, these effects could not be detected after 3 days following pesticide exposure. Overall, our results demonstrate that pesticide exposure adversely affects blood cells, the liver, and the peripheral nervous system. Future studies are needed to elucidate the specific effects of each pesticide and the mechanisms of these effects.