Measles is a highly contagious viral infection associated with clinical symptoms such as fever, cough, conjunctivitis, coryza, eruption and increased serum immunoglobulin M (IgM) antibodies. A clinical diagnosis is easily established when the chain of infection can be followed. However, Japan is currently experiencing sporadic measles outbreaks, which complicate the establishment of diagnosis. Furthermore, other exanthematous infections such as rubella, human parvovirus B19, human herpesvirus 6 (HHV-6) and HHV-7 present with clinical symptoms and IgM antibody levels similar to those in measles. Therefore, real-time polymerase chain reaction virogene testing has been part of Japan's standard diagnostic protocol for measles since 2010. This report presents two pediatric cases clinically resembling measles that were diagnosed as HHV-6 based on a virogene detection test. This underscores the importance of performing pathogen testing to confirm a diagnosis when measles is suspected.