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The development of concepts concerning the role of microglia in different brain diseases has relied on studies of animal models or human brain tissue, which primarily use antibodies and immunohistochemistry techniques to make observations. Since initial studies defined increased expression of the major histocompatibility complex Ⅱ protein human leukocyte antigen-DR as a means of identifying reactive, and therefore by implication, damage-causing microglia in Alzheimer's disease (AD) or Parkinson's disease (PD), understanding and describing their activation states has evolved to an unexpected complexity. It is still difficult to ascertain the specific functions of individual microglia, particularly those associated with pathological structures, using a narrow range of antigenic markers. As many approaches to developing treatments for AD or PD are focused on anti-inflammatory strategies, a more refined understanding of microglial function is needed. In recent years, gene expression studies of human and rodent microglia have attempted to add clarity to the issue by sub-classification of messenger RNA expression of cell-sorted microglia to identify disease-associated profiles from homeostatic functions. Ultimately all newly identified markers will need to be studied in situ in human brain tissue. This review will consider the gaps in knowledge between using traditional immunohistochemistry approaches with small groups of markers that can be defined with antibodies, and the findings from cell-sorted and single-cell RNA sequencing transcription profiles. There have been three approaches to studying microglia in tissue samples: using antigenic markers identified from studies of peripheral macrophages, studying proteins associated with altered genetic risk factors for disease, and studying microglial proteins identified from mRNA expression analyses from cell-sorting and gene profiling. The technical aspects of studying microglia in human brain samples, inherent issues of working with antibodies, and findings of a range of different functional microglial markers will be reviewed. In particular, we will consider markers of microglia with expression profiles that do not definitively fall into the pro-inflammatory or anti-inflammatory classification. These additional markers include triggering receptor expressed on myeloid cells-2, CD33 and progranulin, identified from genetic findings, colony stimulating factor-1 receptor, purinergic receptor P2RY12, CD68 and Toll-like receptors. Further directions will be considered for addressing crucial issues.