The sites of insertion of catheters into the jugular veins of six horses were investigated to determine common isolates and to assess the effectiveness of two disinfection protocols with the hair coat left long, clipped or shaved. Skin commensals (Staphylococcus, Streptococcus and Micrococcus species) and environmental contaminants (Bacillus, Enterobacteriaceae, Aspergillus and Mucor species) were the microorganisms most frequently isolated. Chlorhexidine gluconate and povidone-iodine-based skin disinfection protocols resulted in significant reductions in the number of bacterial isolates from clipped sites. With chlorhexidine, there were no significant differences between the reductions observed at sites with the hair coat left long, clipped or shaved.