Though available evidence is relatively consistent in showing no additional health effects among smokers due to menthol in cigarettes, two studies reported conflicting results for stroke risk using different subsets of NHANES data. We investigated reasons for the differences in these reports by analyzing NHANES cycles conducted between 1999 and 2012, combined and in subsets. Adjusted odds ratios (AOR) and 95% confidence intervals (CI) from three different survey logistic regression models compare risk of reported stroke diagnoses among menthol and non-menthol cigarette smokers. Depending on timeframe, about 1150 to 8000 U.S. adults (aged ≥ 20 years) who smoked on ≥ 1 of the last 30 days had complete data for cigarette type and all covariates included in each model. Results were not much affected by which covariates were included in the models, but depended strongly on the NHANES cycles included in the analysis. Using NHANES 1999–2012 data combined, AORs and 95% CIs for stroke comparing menthol with non-menthol cigarette smokers were 0.95 (95% CI: 0.65, 1.37), 0.85 (95% CI: 0.59, 1.23) or 0.86 (95% CI: 0.59, 1.25). Collectively, findings illustrate the need for fully reporting research and analytical methods, especially when analyses are meant to develop evidence intended for regulatory decision-making.