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Background: A medication-related problem is an event involving medication that interferes with desired health outcomes. Those are largely studied among asthma patients, but little is known about medication-related problems among allergy patients. The objective of this study was to determine the most common patient-reported medication-related problems among asthma patients compared to allergy patients during the self-management of diseases. The other objective was to identify how demographic variables and the received treatment information influence reported problems. Methods: A nationwide survey was conducted in Finnish community pharmacies (n = 785) in September 2016. The survey targeted patients buying prescription medicines for asthma or allergy. Results: Responses were received from 46% of targeted pharmacies from 956 respondents. At least one medication problem was reported by 24% of asthma patients and 12% of allergy patients. The most common problems among asthma patients were having problems taking medicines on time (16%), problems in the administration technique (7%) and in the use of the inhaler (4%). Among allergy patients, 10% reported problems remembering to take medicines on time. Severe asthma and allergy increased the risk for medication-related problems (OR 1.20, 95% CI 1.04–1.40 and OR 1.17, 95% CI 1.0–1.37). A higher age and less education were associated with fewer reported medication-related problems among both patient groups. Conclusions: Asthma patients reported more medication-related problems than allergy patients. Among both investigated patient groups, remembering to take medicines on time was the most common. Health care professionals should educate younger patients but also older and less educated asthma and allergy patients to recognize and, to solve medication-related problems. In addition, severe asthma patients still need medication counseling. [ABSTRACT FROM AUTHOR]