Cat scratch disease (CSD) is caused by Bartonella henselae infection and is a common cause of regional lymphadenopathy. The diagnosis of CSD largely depends on serology, but detection of B. henselae in an affected lymph node by PCR is also an important diagnostic tool. We evaluated an IgM in-house ELISA protocol and analyzed its performance in routine CSD serology. Serum samples from PCR-positive patients (n = 126), PCR-negative patients (n = 123), and age-matched controls (n = 126) were used for evaluation. The sensitivity of the IgM ELISA was only 56%, showing that the performance of B. henselae serology under routine laboratory settings is low, probably caused by the wide variability in disease duration in patients suspected of CSD whose samples were submitted to our laboratory. Most patients (46%) with a positive IgM response were between 0 and 20 years of age. We conclude that the serodiagnosis of B. henselae is hampered by the low sensitivity and specificity of the assays when used in a routine laboratory setting. For this reason, a negative IgM or PCR result can never exclude CSD, especially with late sample collection.