The Mysterium Cosmographicum was a landmark in Kepler's scientific career and, thanks to his revolutionary insights about the sun, in the history of astronomy itself. But the text was not purely "scientific," as the word is meant in the twenty-first century. Chapters of it are filled with astrology, numerology, and mysticism. Even those passages discussing astronomy itself are peppered by references to God and the divine plan.

In the centuries before Kepler, astronomy had been inextricably linked with other studies of the heavens, such as astrology and theology. In the centuries after him, astronomers broke away completely from such things. But in Kepler's era, astronomy was only beginning to turn away from its interdisciplinary nature. More than any astronomer of the time, Kepler and his work represent the contradictions and confusions of this transitional period. Kepler saw no battle between astronomy, religion, and mysticism. For him, each was necessary and had its place. He incorporated each into his work, his theorizing guided alternately by scientific and divine forces.

The discussions of astrology in the Mysterium Cosmographicum reflect Kepler's fascination with the field. Astrology, the study of the stars' effect on human destiny, was popular in the seventeenth century, among both scholars and the public. It usually went hand in hand with astronomy. An astronomer's job often involved interpreting the stars, in addition to observing them.

While at Gratz, it was part of Kepler's job to compile an annual calendar of astrological forecasts. He resented the tedium of the work, as well as the unscientific, superstitious nature of astrology itself. But despite his disdain, Kepler always believed that astrology had scientific potential. He argued that the sky affected man's behavior in some unknown way, and he spent much of his time trying to figure out what that influence might be. The self-analysis he wrote of himself and his family at age twenty-six contained numerous references to astrology. Each person's personality characteristics and major life events were attributed to the stars.

Kepler was not just a reluctant mystic – he was a devout Protestant. His deeply held beliefs assured him that God was ultimately responsible for the structure of the universe, and this idea certainty guided him on his lifelong quest for answers. Tensions over the Copernican system did exist between scientific and religious authorities. But in the age of Kepler, there was still a close bond between the two. Many members of the clergy were also highly acclaimed scientists; similarly, most of the leaders of the Scientific Revolution (such as Copernicus and Newton) were deeply devout. "Science" was rarely referred to by that name – instead it was known as "Natural Philosophy," due to the interrelationship between science, philosophy, theology, and the humanities. The practice of natural philosophy was an all-encompassing pursuit that incorporated both the technical and the divine. Kepler exemplifies this unity.

Kepler was a Protestant, a fact that got him into trouble all his life, as he was continually forced to flee from Catholic persecution. However, it caused him no trouble in terms of his scientific work. Many astronomers and theologians had difficulty reconciling the heliocentric universe to the Bible – which at several points clearly refers to the motion of the sun. If one is to take the Bible as the word of God, then the Copernican theory cannot be physically true. But Kepler glossed over such difficulties – as he argued throughout his career, the Bible is not an astronomical text, and should not be taken as such. Any astronomical comments in the Bible are merely figures of speech, according to Kepler, and should be taken as such.

Though he carefully attempted to separate astronomical teachings from holy writings, Kepler firmly believed that the study of the stars was the study of God's plan. He was driven to develop his theory of the perfect solids because he believed that God must have imposed some discernable pattern on the universe. This is a constant refrain throughout his life's work. Kepler remained convinced that through astronomical study, he could come to understand the mind of God. For Kepler, while science and theology may have been two distinct disciplines, astronomy and God were one and the same. As he wrote in the introduction of the Mysterium Cosmographicum, "The ideas of quantities have been and are in God from eternity, they are God himself" For Kepler, God was in the numbers.