Diagnosis of strongyloidosis is sometimes problematic and requires novel techniques. Here, critical diagnosis of a complicated case of strongyloidosis using molecular methods is reported. A young woman referred to the Diagnostic Laboratory of Strongyloidiasis in School of Public Health, Tehran University of Medical Sciences. She had taken albendazole before referring to the laboratory. She had cerebral edema, behavior disorders, hypereosinophilia and titer of IgE >2000 IU/mL. The patient had history of intestinal and skin disorders and steroid therapy. For detection of Strongyloides stercoralis infection, parasitological techniques and novel methods of nested-PCR and HRM analysis were applied on stool samples upon admission and during the following up. On the samples provided upon first admission, parasitology showed negative results, while both molecular methods revealed infection with S. stercoralis. After specific treatment, during the following up, the patient general health was much improved and the results of all parasitological and molecular tests were negative for strongyloidosis. Application of novel sensitive diagnostic methods for detection of S. stercoralis is necessary, especially once parasitological techniques have lack of sensitivity.