Allelic variants of CYP1A1 and PON1 have been extensively studied as susceptibility factors in toxic response, although little is known about the role of these variants as risk factors for the plethora of diseases appearing in the human population. In this study we investigated the hypothesis of correlation of CYP1A1 and PON1 enzymes with the incidence of various medical examination findings in a Greek rural population professionally exposed to a variety of pesticides. The medical history of 492 individuals, randomly selected for the total population of 42,000, was acquired by interviews and their genotype determined for the CYP1A1*2A, PON1 M/L and PON1 Q/R polymorphisms. The assessment of exposure to pesticides of the population was verified by analytical methods. Analysis of the genetic data revealed that the allele frequencies of PON1 R, M and CYP1A1*2A alleles were 0.243, 0.39 and 0.107 respectively. The CYP1A1*2A polymorphism was found to have significant association with chronic obstructive pneumonopathy (p=0.045), peripheral circulatory problems (trend p=0.042), arteritis (p=0.022), allergies (trend p=0.046), hemorrhoids (trend p=0.026), allergic dermatitis (p=0.0016) and miscarriages (p=0.012). The PON1 Q/R polymorphism was found to have significant association with hypertension (p=0.046) and chronic constipation (p=0.028) whereas, the L/M polymorphism, with diabetes (p=0.036), arteritis (trend p=0.022) and hemorrhoids (trend p=0.027). Our results demonstrated an association between the CYP1A1/PON1 polymorphisms and several medical examination findings, thus indicating the possible involvement of the human detoxification system to health effects in a rural population exposed professionally to pesticides.