This paper presents an analysis of the hygiene management based on the compliance with the prerequisites of a HACCP system in 53 agri-food industries operating in the department of Huila in Colombia. The evaluation methodology corresponded to the verification of the compliance of checklists for two instruments: GHYCAL (Management of Hygiene and Quality) and SQ 12 companies in basic compliance level, to obtain ratings from 75 % to 95 %, and 7 companies with higher compliance level, with evaluations higher than 95 %; additionally the similarities and differences between companies and between the sectors studied, using multivariate statistical analysis, were assessed.