Emerging evidence indicates that cellular mechanical behavior can be altered by disease, drug treatment, and mechanical loading. To effectively investigate how disease and mechanical or biochemical treatments influence cellular mechanical behavior, it is imperative to determine the source of large inter-cell differences in whole-cell mechanical behavior within a single cell line. In this study, we used the atomic force microscope to investigate the effects of cell morphological parameters and confluency on whole-cell mechanical behavior for osteoblastic and fibroblastic cells. For nonconfluent cells, projected nucleus area, cell area, and cell aspect ratio were not correlated with mechanical behavior (p ≥ 0.46), as characterized by a parallel-spring recruitment model. However, measured force-deformation responses were statistically different between osteoblastic and fibroblastic cells (p < 0.001) and between confluent and nonconfluent cells (p < 0.001). Osteoblastic cells were 2.3-2.8 times stiffer than fibroblastic cells, and confluent cells were 1.5-1.8 times stiffer than nonconfluent cells. The results indicate that structural differences related to phenotype and confluency affect whole-cell mechanical behavior, while structural differences related to global morphology do not. This suggests that cytoskeleton structural parameters, such as filament density, filament crosslinking, and cell-cell and cell-matrix attachments, dominate inter-cell variability in whole-cell mechanical behavior.