 During the period when philosophy of science focused primarily on laws, cell biology was largely neglected. Although it is important to cell biologists to discover useful generalizations, these are seldom characterized as laws. Once philosophers of science turned their attention from laws to mechanisms, from representational realism to models and their functionality, and from concepts and theories to experiments and instrumentation, more philosophers of science have turned their attention to the practices of cell biology. These practices are epistemically challenging. Due to the fact that cells are mostly microscopic, they raise traditional philosophical issues concerning the status of unobservables and the trustworthiness of evidence. Since a major concern of cell biology is to relate functions (e.g., biochemical reactions) to cell structures, cell biologists need not just to observe but also to physically manipulate cells and their constituent structures and to develop informative representations. Their activities thus provide rich examples for philosophers. Although a great deal of cell biology has yet to be tapped for philosophical analysis, we provide examples in which philosophers (as well as historians) have investigated and analyzed material practices in cell biology. We start, however, closer to theoretical interests, examining how the discipline of cell biology developed and how metaphors have played crucial roles in shaping how scientists have conceptualized cells. Subsequently we turn to controversies over whether cells can be understood mechanistically or require a vitalist or holist perspective. After that, we turn to questions of epistemology, including strategies for representing cells visually and for developing mechanistic accounts of cell functioning.