How can citation analysis take into account the highly collaborative nature and unique research and publication culture of biomedical research fields? This study explores this question by introducing last-author citation counting and comparing it with traditional first-author counting and theoretically optimal all-author counting in the stem cell research field for the years 2004–2009. For citation ranking, last-author counting, which is directly supported by Scopus but not by ISI databases, appears to approximate all-author counting quite well in a field where heads of research labs are traditionally listed as last authors; however, first author counting does not. For field mapping, we find that author co-citation analyses based on different counting methods all produce similar overall intellectual structures of a research field, but detailed structures and minor specialties revealed differ to various degrees and thus require great caution to interpret. This is true especially when authors are selected into the analysis based on citedness, because author selection is found to have a greater effect on mapping results than does choice of co-citation counting method. Findings are based on a comprehensive, high-quality dataset extracted in several steps from PubMed and Scopus and subjected to automatic reference and author name disambiguation.