Numerous long-term monitoring programs have assessed spatial and temporal trends of organochlorine (OC) pesticides and polychlorinated biphenyls (PCBs). Changes in analytical approaches (e.g., gas chromatography coupled with electron capture detection [GC-ECD] versus mass spectrometric detection [GC-MSD]) can reveal artifacts in the reported concentrations. In-house reference material (RM) was used to determine the analytical artifacts in the measurement of OCs and PCBs in Great Lake herring gull eggs previously analyzed from 1994 to 1996 (GC-ECD) and 1997 to 1999 (GC-MSD). Approximately 19.0% of the variability of PCB congeners in gull eggs was associated with analytical artifacts, and differences among colonies were obscured. Although the discrepancy in sum PCBs (SigmaPCBs) was fairly small (2.1%), some congeners varied considerably between methods (> 60%). After statistically removing the artifacts, only 1.4% of the variability in PCBs of herring gull eggs was associated with artifacts, and differences among gull colonies became apparent. After excluding OCs near the detection limit in the RM, statistically removing the artifacts reduced some of the differences between methods for OCs. Analytical artifacts may potentially render inferences difficult, confounded, and erroneous. When combining contaminant data obtained using different methods, the methods should be assumed to give different results unless demonstrated otherwise. Assessments of the compatibility of analytical methodologies should be made using an appropriate RM.