A 24-year-old HIV-positive heterosexual woman with disseminated cryptosporidiosis was monitored from January 1998 to May 1999. During this period, consecutive stool, sputum, and bile examinations showed the constant presence of Cryptosporidium oocysts. Although the patient was repeatedly treated with oral paromomycin and azithromycin and, finally, nitazoxanide, her condition continued to deteriorate. In order to monitor the in vitro susceptibility of the parasite, specimens from various sites were collected periodically. When the first clinical isolate was tested, the antimicrobial agents used (azithromycin at a concentration of 8 mg/l, paromomycin at of 1 mg/ml, and nitazoxanide at 10 mg/l) produced a decrease in parasite counts of 26.5%, 63.4%, and 67.2%, respectively. Subsequent isolates of Cryptosporidium parvum showed similar susceptibilities. This case demonstrates that failure of clinical treatment corresponded to inadequate growth inhibition of the parasite in vitro.