Background: Migraine is a complex neurological disorder with high co-existing morbidity burden. The aim of our study was to examine the overall morbidity and phenotypic diseasome for migraine among people of working age using real world data collected as a part of routine clinical practice. Methods: Electronic medical records (EMR) of patients with migraine (n = 17,623) and age-and gender matched controls (n = 17,623) were included in this retrospective analysis. EMRs were assessed for the prevalence of ICD-10 codes, those with at least two significant phi correlations, and a prevalence >2.5% in migraine patients were included to phenotypic disease networks (PDN) for further analysis. An automatic subnetwork detection algorithm was applied in order to cluster the diagnoses within the PDNs. The diagnosis-wise connectivity based on the PDNs was compared between migraine patients and controls to assess differences in morbidity patterns. Results: The mean number of diagnoses per patient was increased 1.7-fold in migraine compared to controls. Altogether 1337 different ICD-10 codes were detected in EMRs of migraine patients. Monodiagnosis was present in 1% and 13%, and the median number of diagnoses was 12 and 6 in migraine patients and controls. The number of significant phi-correlations was 2.3-fold increased, and cluster analysis showed more clusters in those with migraine vs. controls (9 vs. 6). For migraine, the PDN was larger and denser and exhibited one large cluster containing fatigue, respiratory, sympathetic nervous system, gastrointestinal, infection, mental and mood disorder diagnoses. Migraine patients were more likely affected by multiple conditions compared to controls, even if no notable differences in morbidity patterns were identified through connectivity measures. Frequencies of ICD-10 codes on a three character and block level were increased across the whole diagnostic spectrum in migraine. Conclusions: Migraine was associated with an increased multimorbidity, evidenced by multiple different approaches in the study. A systematic increase in the morbidity across the whole spectrum of ICD-10 coded diagnoses, and when interpreting PDNs, were detected in migraine patients. However, no specific diagnoses explained the morbidity. The results reflect clinical praxis, but also undoubtedly, the pathophysiological phenotypes related to migraine, and emphasize the importance of better understanding migraine-related morbidity.