Microsporidia are currently considered emerging pathogens responsible for life-threatening infections in organ transplant recipients. Here, we describe the first cases of intestinal microsporidiosis by Enterocytozoon bieneusi genotype D in two non-HIV-infected renal transplant recipients from Spain. Previously reported cases of microsporidiosis in organ transplant recipients have also been reviewed, highlighting the necessity of considering organ transplant recipients a risk group for microsporidiosis. A systematic search for these parasites is recommended in cases of persistent diarrhea and in the differential diagnosis of other syndromes, such as chronic fever of unknown etiology.