The properties Of lipid bilayer nanometer-scale domains could be crucial for understanding Cell, membranes: Fluorescent probes are often used to study bilayers, yet:their effects on host lipids are not well understood. We used molecular dynamics simulations to investigate perturbations in a fluid DPPC bilayer upon incorporation Of three indocarbocyanine probes: DiI-C18:0; DiI-C18:2, or DiI-C12:0. We find a 10-12% decrease in chain order for DPPC in the solvation shell nearest the probe but smaller effects in subsequent shells, indicating that the probes significantly alter only their local environment. We also observe order perturbations of lipids directly across from the probe in the opposite leaflet Additionally, the DPPC headgroup phosphorus-to-nitrogen vector of lipids nearest the probe exhibits preferential orientation pointing away from the DiI. We show that, while DiI probes perturb their local, environment, they do not strongly influence. the average properties of "nanoscopic" domains containing a few hundred lipids.