Introduction: The occupational toxic risks from agricultural activities in El Salvador affect human and environmental health. The objective of this paper is to describe the management of pesticide by farmers confirmed with a chronic kidney disease of uncertain etiology (CKDu) not associated to diabetes mellitus or hypertension. Methods: The study involved 42 male patients older than 18 years old with confirmed CKDu that have participated in different stages of pesticides management. This is a cross-sectional study; it was conducted from January to June 2011, in three communities of Bajo Lempa region, El Salvador. An interview was especially designed to investigate which pesticides were used and the farmer practices at different stages of pesticide use. Statistical descriptive analysis was carried out for the several studied variables. Results: All interviewed people had a direct relationship with agricultural activities. The majority of patients had poor education, 19% were illiterate and 55% only have primary education. Most farmers with CKDu had been exposed more than 10 years to hazardous pesticides. The most used pesticide was Hedonal/2, 4 D (100%). 95% interviewed patients mixed different pesticides and 63% dumped empty pesticide containers in the fields. Interviewees did not use appropriate personal protective equipment (100%). Conclusions: There is high use of hazardous pesticides by patients and some of these are banned and some are legal in El Salvador, but prohibited by other countries. Interviewed CKDu patients had high exposure to toxic pesticides due to the misuse in almost all stages. There is inadequate legislation and a poor law enforcement to prevent the misuse of pesticides in El Salvador.