Macrophages play an important role in clearing apoptotic debris from tissue. Defective or reduced clearance, seen, for instance in non-obese diabetic (NOD) mice has been correlated with initiation of autoimmune (type 1) diabetes (T1D) (OBrien et al., 2002b). To validate such a link, it is essential to quantify the reduced clearance (for example, by comparison to BALB/C control mice), and to determine which elements of that clearance are impaired. Recently, we fit data for the time course of in vitro macrophage feeding experiments to basic models of macrophage clearance dynamics, thus quantifying kinetics of uptake and digestion of apoptotic cells in both mouse strains (Mar?ee et al., 2005). In the cycle of modeling and experimental investigation, we identified the importance of (1) measuring short, intermediate, and long-time data (to increase the accuracy of parameter fits), and (2) designing experiments with distinct observable regimes, including engulfment-only and digestion-only phases. Here we report on new results from experiments so designed. In comparing macrophages from the two strains, we find that NOD macrophage engulfment of apoptotic cells is 5.5 times slower than BALB/C controls. Significantly, our new data demonstrates that digestion is at least 2 times slower in NOD, in contrast with previous conclusions. Moreover, new data enables us to detect an acceleration in engulfment (after the first engulfment) in both strains, but much smaller in NOD macrophages.