In biology, cell theory is a scientific theory first formulated in the mid-nineteenth century, that living organisms are made up of cells, that they are the basic structural/organizational unit of all organisms, and that all cells come from pre-existing cells. Cells are the basic unit of structure in all living organisms and also the basic unit of reproduction.

Cell theory has traditionally been accepted as the governing theory of all life, but some biologists consider non-cellular entities such as viruses living organisms and thus disagree with the universal application of cell theory to all forms of life.

With continual improvements made to microscopes over time, magnification technology became advanced enough to discover cells. This discovery is largely attributed to Robert Hooke, and began the scientific study of cells, known as cell biology. When observing a piece of cork under the scope, he was able to see pores. This was shocking at the time as it was believed no one else had seen these. To further support his theory, Matthias Schleiden and Theodor Schwann both also studied cells of both animal and plants. What they discovered were significant differences between the two types of cells. This put forth the idea that cells were not only fundamental to plants, but animals as well.

The discovery of the cell was made possible through the invention of the microscope. In the first century BC, Romans were able to make glass. They discovered that objects appeared to be larger under the glass. The expanded use of lenses in eyeglasses in the 13th century probably led to wider spread use of simple microscopes (magnifying glasses) with limited magnification. Compound microscopes, which combine an objective lens with an eyepiece to view a real image achieving much higher magnification, first appeared in Europe around 1620. In 1665, Robert Hooke used a microscope about six inches long with two convex lenses inside and examined specimens under reflected light for the observations in his book Micrographia. Hooke also used a simpler microscope with a single lens for examining specimens with directly transmitted light, because this allowed for a clearer image.

An extensive microscopic study was done by Anton van Leeuwenhoek, a draper who took the interest in microscopes after seeing one while on an apprenticeship in Amsterdam in 1648. At some point in his life before 1668, he was able to learn how to grind lenses. This eventually led to Leeuwenhoek making his own unique microscope. He made one with a single lens. He was able to use a single lens that was a small glass sphere but allowed for a magnification of 270x. This was a large progression since the magnification before was only a maximum of 50x. After Leeuwenhoek, there was not much progress in microscope technology until the 1850s, two hundred years later. Carl Zeiss, a German engineer who manufactured microscopes, began to make changes to the lenses used. But the optical quality did not improve until the 1880s when he hired Otto Schott and eventually Ernst Abbe.

Optical microscopes can focus on objects the size of a wavelength or larger, giving restrictions still to advancement in discoveries with objects smaller than the wavelengths of visible light. The development of the electron microscope in the 1920s made it possible to view objects that are smaller than optical wavelengths, once again opening up new possibilities in science.

The cell was first discovered by Robert Hooke in 1665, which can be found to be described in his book Micrographia. In this book, he gave 60 observations in detail of various objects under a coarse, compound microscope. One observation was from very thin slices of bottle cork. Hooke discovered a multitude of tiny pores that he named "cells". This came from the Latin word Cella, meaning ‘a small room’ like monks lived in, and also Cellulae, which meant the six-sided cell of a honeycomb. However, Hooke did not know their real structure or function. What Hooke had thought were cells, were actually empty cell walls of plant tissues. With microscopes during this time having a low magnification, Hooke was unable to see that there were other internal components to the cells he was observing. Therefore, he did not think the "cellulae" were alive. His cell observations gave no indication of the nucleus and other organelles found in most living cells. In Micrographia, Hooke also observed mould, bluish in color, found on leather. After studying it under his microscope, he was unable to observe "seeds" that would have indicated how the mould was multiplying in quantity. This led to Hooke suggesting that spontaneous generation, from either natural or artificial heat, was the cause. Since this was an old Aristotelian theory still accepted at the time, others did not reject it and was not disproved until Leeuwenhoek later discovered that generation was achieved otherwise.

Anton van Leeuwenhoek is another scientist who saw these cells soon after Hooke did. He made use of a microscope containing improved lenses that could magnify objects 270-fold. Under these microscopes, Leeuwenhoek found motile objects. In a letter to The Royal Society on October 9, 1676, he states that motility is a quality of life therefore these were living organisms. Over time, he wrote many more papers which described many specific forms of microorganisms. Leeuwenhoek named these "animalcules," which included protozoa and other unicellular organisms, like bacteria. Though he did not have much formal education, he was able to identify the first accurate description of red blood cells and discovered bacteria after gaining interest in the sense of taste that resulted in Leeuwenhoek to observe the tongue of an ox, then leading him to study "pepper water" in 1676. He also found for the first time the sperm cells of animals and humans. Once discovering these types of cells, Leeuwenhoek saw that the fertilization process requires the sperm cell to enter the egg cell. This put an end to the previous theory of spontaneous generation. After reading letters by Leeuwenhoek, Hooke was the first to confirm his observations that were thought to be unlikely by other contemporaries.