Partially premixed combustion strategies offer many advantages for compression ignition engines. One such advantage for engines operating on diesel fuels is the simultaneous reduction of soot and NOx achievable over a wide range of equivalence ratios. Though often not measured in engine experiments, gaseous H2 is a byproduct of incomplete combustion and can be useful for the regeneration of aftertreatment devices. Correlations for the exhaust concentration of H2, mostly derived from experiments with homogeneous spark ignition engines, indicate that it is emitted either in proportion to CO directly or as a function of a pseudo-water gas shift equilibrium constant. In this work, H2 is measured over a range of equivalence ratios in a multi-cylinder diesel engine operating in a partially premixed low temperature combustion (LTC) mode using both low sulfur diesel fuel and soy-based biodiesel. Biodiesel was found to have the same bulk gas emissions of major species including H2 over the range of equivalence ratio in LTC for a constant load and combustion phasing. It also was found that the experimental H2 concentration was near the value predicted by the equilibrium constant for equivalence ratios greater that 0.9 but was increasingly lower for leaner points.