In the United States, federally-funded health plans are mandated to measure the quality of care. Adherence-based medication quality metrics depend on completeness of administrative claims data for accurate measurement. Low-cost generic programs (LCGPs) cause medications fills to be missing from claims data as medications are not adjudicated through a patient's insurance. This study sought to assess the magnitude of the impact of LCGPs on these quality measures. Data from the 2012-2013 Medical Expenditure Panel Survey (MEPS) were used. Medication fills for select medication classes were classified as LCGP fills and individuals were classified as never, sometimes, and always users of LCGPs. Individuals were classified based on insurance type (private, Medicare, Medicaid, dual-eligible). The proportion of days covered (PDC) was calculated for each medication class and the proportion of users with PDC 0.80 was reported as an observed metric for what would be calculated based on claims data and a true metric which included missing medication fills due to LCGPs. True measures of adherence were higher than the observed measures. The effect's magnitude was highest for private insurance and for medication classes utilized more often through LCGPs. Thus, medication-based quality measures may be underestimated due to LCGPs.