Objective: Information on borderline personality disorder (BPD) and its comorbidities is often limited to concentrate on a few diagnoses. The aim of the study was to use national register data to investigate all diagnostic co-occurring mental health disorders and somatic diseases 3 years before and after initial BPD diagnosis compared with a matched control group. Method: The study was a register-based cohort of 2756 patients with incident BPD (ICD F60.3) and 11,024 matched controls, during 2002–2016. Comorbidity data were classified into main disease groups, in accordance with the World Health Organization ICD-10 criteria. Results: Almost half the patients had been diagnosed with mental and behavioral disorders before the BPD diagnosis as compared to 3% in the control group. Further, the co-occurrence of diseases due to external causes of morbidity, including injury, self-harm, and poisoning were more represented in the BPD group before diagnosis as compared to the control group. In addition, co-occurring morbidity related to diseases in the circulatory, the respiratory, the digestive, the musculoskeletal, and the genitourinary system was more represented in the BPD group. After diagnosis, the proportion of patients with co-occurring morbidity increased further in all main disease groups in the BPD group. As many as 87% of patients had mental and behavioral co-occurring morbidity and 15% nervous diseases as compared with 3% and 4%, respectively, in the control group. Also, comorbidities related to external causes of morbidity, including for example, injury and self-harm were more represented in the BPD group. The BPD group had more somatic co-occurring morbidity, especially digestive, respiratory, circulatory, and endocrine diseases. Finally, the mortality over 12 years was statistically significantly higher in people with BPD than in the control group. Conclusion: Patients with BPD have higher odds for multiple physical health conditions and co-occurrence of mental health disorders.