Prevalences of multimorbidity vary between European studies and several methods and definitions are used. In this study we examine the prevalence of multimorbidity in relation to age, gender and educational attainment and the association between physical and mental health conditions and educational attainment in a Danish population. A cross-sectional design was used to study the prevalence of multimorbidity, defined as two or more chronic conditions, and of comorbid physical and mental health conditions across age groups and educational attainment levels among 1,397,173 individuals aged 16 years and older who lived in the Capital Region of Denmark on January 1st, 2012. After calculating prevalence, odds ratios for multimorbidity and mental health conditions were derived from logistic regression on gender, age, age squared, education and number of physical conditions (only for odds ratios for mental health conditions). Odds ratios for having multimorbidity and mental health conditions for each variable were adjusted for all other variables. Multimorbidity prevalence was 21.6%. Half of the population aged 65 and above had multimorbidity, and prevalence was inversely related to educational attainment: 26.9% (95% CI, 26.8–26.9) among those with lower secondary education versus 13.5% (95% CI, 13.5–13.6) among people with postgraduate education. Adjusted odds ratios for multimorbidity were 0.50 (95% CI, 0.49–0.51) for people with postgraduate education, compared to people with lower secondary education. Among all population members, 4.9% (95% CI, 4.9–4.9) had both a physical and a mental health condition, a proportion that increased to 22.6% of people with multimorbidity. Physical and mental health comorbidity was more prevalent in women (6.33%; 95% CI, 6.3–6.4) than men (3.34%; 95% CI, 3.3–3.4) and approximately 50 times more prevalent among older persons than younger ones. Physical and mental health comorbidity was also twice as prevalent among people with lower secondary education than among those with postgraduate education. The presence of a mental health condition was strongly associated with the number of physical conditions; those with five or more physical conditions had an adjusted odds ratio for a mental health condition of 3.93 (95% CI, 3.8–4.1), compared to those with no physical conditions. Multimorbidity prevalence and patterns in the Danish population are comparable to those of other European populations. The high prevalence of mental and physical health conditions highlights the need to ensure that healthcare systems deliver care that takes physical and mental comorbidity into account. Further, the higher prevalence of multimorbidity among persons with low educational attainment emphasizes the importance of having a health care system providing care that is beneficial to all regardless of socioeconomic status.