Intracellular calcium ion (Ca2+) changes in NIH-3T3 fibroblasts responding to inositol 1,4,5-trisphosphate (IP3) injections have been monitored using high resolution digital imaging of the calcium indicator Fura-2. Ester loaded and microinjected indicator report radically different patterns of Ca2+ change during the IP3 response. These differences arise from intracellular compartmentalization of the ester loaded indicator which can seriously distort reported Ca2+ levels. Prominent among these aberrant responses is a signal in which Ca2+ levels in the cell nucleus appear to exceed those in the rest of the cell, and an apparent slowing of the Ca2+ recovery time-course throughout the cell when temperature is increased. Similar behavior is observed in other cell types. Judicious use of both loading techniques can provide information on Ca2+ movements into organelles that might otherwise escape detection. The Ca2+ rise normally measured in bulk or integrated single cell measurements is a complex mix of cytosol/nucleus and organellar changes. Much, if not all, of the observable organellar change is an accumulation, not release, of Ca2+ following the IP3 injection. The Golgi apparatus is a conspicuous early site for this accumulation, and mitochondria show a large, temperature sensitive uptake that is capable of limiting the maximal Ca2+ change during the response.