A five-to-ten fold enhancement, up to ca. 5-10% quantum efficiency, of near IR luminescence from monothiolate protected gold nanoclusters was achieved by heating in the presence of excess ligand thiols. An emission maximum in the 700-900 nm range makes these Au nanoclusters superior for bioimaging applications over other emissions centered below 650 nm due to reduced background interference, albeit visible emissions could have higher quantum efficiency. The heating procedure is shown to be effective to improve the luminescence of Au nanoclusters synthesized under a variety of conditions using two types of monothiols: mercaptosuccinic acid and tiopronin. Therefore, this heating method is believed to be a generalizable approach to improve the near IR luminescence of aqueous soluble Au nanoclusters, which enables better bioimaging applications. The high quantum yield is found relatively stable over a wide pH range. PEGylation of the Au nanoclusters reduces their quantum efficiency but improves their permeation into the cytoplasm. Interestingly, z-stack confocal analysis clearly reveals the presence of Au nanoclusters inside the cell nucleus in single cell imaging. The finding addresses controversial literature reports and demonstrates the internalization and heterogeneous subcellular distributions, particularly inside the nucleus. The high luminescence intensity, small overall dimension, cell and nuclear distribution, chemical stability and low-to-non toxicity make these Au nanoclusters promising probes for broad cell dynamics and imaging applications.