Nine naturally infected asymptomatic budgerigars (Melopsittacus undulatus) were screened daily for microsporidia spore excretion during a 30-day period and the localization of infection was evaluated using microscopy and molecular methods. While the microscopic examination revealed 2.4% positivity out of all fecal samples, using PCR the positivity was 10x higher (24.6%). All nine budgerigars excreted microsporidial spores intermittently in irregular intervals with 1-11-day long interruptions. Most of the birds were infected simultaneously with Encephalitozoon cuniculi and Encephalitozoon hellem. While histological and TEM examination failed to confirm the presence of microsporidial spores in tissues, the PCR detected microsporidial DNA mostly in the small intestine, liver and lungs of four selected budgerigars dissected. Despite the chronic infection proved using molecular methods, no clinical signs of disease were observed during monitoring and no pathological findings were found during dissection.