Pesticides are chemicals used to control pests with sometime harmful effects on human health. This paper presents results of self-reported health effects experienced by cotton farmers in the Central-West region of Burkina Faso. It was a cross-sectional survey conducted from October to December 2021 among 585 consenting conventional and organic cotton farmers. Data collected included pesticides used, they use conditions, farming practices, experienced health effects. Binary logistic regression was used to find relationships between selfreported health effects and the type of cotton produced. Results showed that all conventional cotton farmers (100%) reported using synthetic pesticides compared to organic ones who using only natural insecticides. Both conventional and organic farmers reported health effects that occurred at least once since they started using pesticides, involving skin effects (85.27% conventional, 65.52% organic), nervous (88.95% conventional, 48,71% organic), respiratory (88.10% conventional, 67.67% organic) systems. 99.72% of conventional farmers vs 46.98% of organic ones reported skin irritation following pesticide use. 69.97% of conventional vs 35.34% of organic cotton farmers reported acute signs such as severe headaches. In univariate and multivariate logistic regressions, severe headaches, dizziness, skin, and ocular effects were significantly associated with conventional farmers compared to organic ones (p < 0.05). There was a significant relationship between vomiting (p = 0.014), diarrhea (p = 0.003) and experience in synthetic pesticide use among conventional farmers. Among organic farmers, there was no significant relationship between health effects reported and experience in organic insecticides use. there was a significant relationship between severe headaches (p = 0.01), rhinitis (p = 0.006), cough (p = 0.0001), skin and ocular irritations (p = 0.007) and the frequency of synthetic insecticides use per year by conventional farmers. Study showed that conventional and organic cotton producers experience the same types of health effects. However, these health effects were significantly associated with conventional farmers compared to organic ones.