Background Handling of unavailable prescriptions, i.e. prescriptions missing on the online server, is considered troublesome and time-consuming by community pharmacy staff and may result in both patient dissatisfaction and non-compliance. Objective To describe the occurrence and reasons for unavailable prescriptions at Danish community pharmacies as well as the types of drugs involved. Method An online 11-item questionnaire was developed and distributed to 24 community pharmacies across Denmark which each collected data on unavailable prescriptions handled within a 3-week period. Results Out of 194,358 prescriptions dispensed during the study period, a total of 2765 (1.4%) unavailable prescriptions were registered. Of these, 51.1% (n = 1412) occurred when a patient expected a new prescription after having consulted a physician, most often the patient's general practitioner (75.6%; n = 1067). Of all unavailable prescriptions, 68.1% (n = 1882) concerned prescriptions on regular drugs for treatment of a chronic condition, with the patient not having any medication left in 27.9% (n = 526) of these cases. Unavailable prescriptions most frequently concerned cardiovascular drugs (15.8%; n = 437) followed by nervous system drugs (14.4%; n = 399). Conclusion Unavailable prescriptions occur in approximately 1% of all dispensing at Danish community pharmacies. Miscommunication between the patient and general practitioner seems to be the primary source of unavailable prescriptions.