Two baddeleyite megacrysts were evaluated as potential reference materials (RMs) for SIMS oxygen isotope analysis, and utilized to understand and calibrate instrumental mass fractionation (IMF). A baddeleyite crystal (S0045) from the Phalaborwa carbonatite, South Africa has a mean δ18OVSMOW=+4.6 ± 0.3‰(range 0.75‰) measured using laser fluorination gas source mass spectrometry (LF-GMS) and one (S0069) from the Mogok metamorphic belt, Myanmar has δ18OVSMOW=+22.2 ± 0.4‰ (range 0.89‰). SIMS standardization utilizing these inherently heterogeneous RMs is possible by analyzing a number of crystal fragments and utilizing one of them lying at the median of the range. Metamictization, lattice orientation, and chemical composition do not appear to be significant (< 0.5‰) variables in matrix matching of RMs and unknowns. Propagation of errors while utilizing the imperfect RMs results in 10 μm diameter spot uncertainties of about±0.3‰ (2σ). SIMS oxygen isotope analysis of co-crystalline zircon and baddeleyite from the 2.2 Ga Duck Lake sill (DLS) in the Northwest Territories, Canada, yield predominant δ18OVSMOW modes of +6.0‰ and +3.2‰, respectively. This difference is consistent with preserving high-temperature isotopic equilibrium between zircon and baddeleyite. DLS baddeleyite δ18O data as a whole are negatively skewed (to 0.0‰), and interpreted to reflect low temperature, open-system behaviour. Zircon δ18O are less affected, but also show hints of the same influences of secondary alteration and oxygen isotope exchange.