Isospora belli is an opportunistic protozoon which should be monitored in patients with gastrointestinal complaints such as abdominal pain, nausea and diarrhoea, in both immune-compromised and immune-competent patients. Our case was a 35 year-old male patient who had received a liver transplant because of cirrhosis and hepatic fibrosis. A diarrhoeic stool sample of the patient was sent to the laboratory for microbiological and parasitological analyses. Faecal occult blood was positive and bacteriological analysis was negative. Isospora belli infection was diagnosed by detection of the oocysts in stool samples. Per oral trimethoprim-sulphamethoxazole treatment was given in 500 mg bid dose for 10 days. At the end of the treatment, no oocyst of Isospora belli was seen but non-pathogenic cysts of Entamoeba coli and vacuolar forms of Blastocystis hominis were observed. Two months later the patient had abdominal pain, fatigue and diarrhoea again and parasitological re-evaluation showed oocysts of Isospora belli.