Purpose: To explain the controversy about whether midlife women who self-report hot flashes have relatively increased affective symptoms, poor cognitive performance or worse sleep. Methods: Retrospective data from 88 women seeking relief from bothersome day and night hot flashes were submitted to mixed linear regression modeling to find if estimated hot flashes, as measured by Women's Health Questionnaire (WHQ) items, or diary-documented hot flashes recorded daily, were associated with each other, or with affective, cognitive or sleep measures. Results: Subjects averaged 6.3 daytime diary-documented hot flashes and 2.4 nighttime diary-documented hot flashes per 24 h. Confounder-controlled diary-documented hot flashes but not estimated hot flashes were associated with increased Leeds anxiety scores (F=4.9; t=2.8; p=0.01) and Leeds depression scores (3.4; 2.5; 0.02), decreased Stroop Color Word test performance (9.4; 3.5; 0.001), increased subjective sleep disturbance (effect size = 0.83) and increased objective sleep disturbance (effect size = 035). Hot flash effects were small to moderate in size. Univariate but not multivariate analyses revealed that all hot flash measures were associated with all affect measures. Different measures of hot flashes associated differently with affect, cognition and sleep. Only nighttime diary-document hot flash consistently correlated with any affect measures in multivariate analyses. Conclusions: The use of differing measures for hot flashes, affect, cognition and sleep may account for the continually reported inconsistencies in menopause study outcomes. This problem impedes forging a consensus on whether hot flashes correlate with neuropsychological symptoms. (C) 2015 Elsevier Ireland Ltd. All rights reserved.