In HIV-1 infected patients severe enteritis and chronic diarrhea are often documented as a consequence of multiple opportunistic infections. We analyzed 48 HIV-1 positive patients for the presence of intestinal pathogenic protozoa. Patients with CD4 > or = 200/mm3 showed a higher prevalence of a single pathogenic protozoa than patients with CD4 < or =200/mm3, who showed the presence of multiple protozoal infections. Patients who proved positive for only a single protozoa, Cryptosporidium or Blastocystis, were also positive, by stool culture, for the presence of Proteus mirabilis (3 samples), Citrobacter freundii (3 samples), Escherichia coli (one sample) or Enterobacter cloacae (one sample). Treatment with rifaximin (600 mg, 3 times a day, for 14 days) was efficacious in resolving the clinical symptoms and clearing protozoan infections in HIV-1 infected patients with CD4 > or = 200/mm3, who presented enteric and systemic symptoms due to Criptosporidium or Blastocystis associated with enteropathogenic bacteria.