In order to compare the prevalence of intestinal microsporidiosis in children with severe malnutrition and eutrophic children at the Nutritional Recovery Unit, Chiquinquirá Hospital in Maracaibo, State of Zulia, a chain reaction technique was performed on the polymerase (PCR) to identify Encephalitozoon intestinalis and Enterocytozoon bieneusi in stool samples from 50 healthy and 50 severely malnourished children, whose ages were stratified as follows: younger infants (0-11 months), older infants (12-23 months), preschool (2-6 years) and school children (7-12 years). Of the microsporidia species investigated, Enterocytozoon bieneusi was evident in 14% of severely malnourished children and 8% of the eutrophic children. No amplifications for Encephalitozoon intestinalis were obtained in the groups studied. On applying the chi-square statistical test, the result was not significant for the variables intestinal microsporidiosis and malnutrition. Conclusions are that the extent to which malnutrition and microsporidiosis relate is difficult to clarify, because malnutrition is a multifactorial condition, and it is not yet well established which of these two factors is the cause and which is the consequence.