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The diagnosis and management of insomnia relies primarily on clinical history. However, patient self-report of sleep-wake times may not agree with objective measurements. We hypothesized that those with shallow or fragmented sleep would under-report sleep quantity, and that this might account for some of the mismatch. We compared objective and subjective sleep-wake times for 277 patients who underwent diagnostic polysomnography. The group included those with insomnia symptoms (n = 92), obstructive sleep apnea (n = 66) or both (n = 119). Mismatch of wake duration was context dependent: all three groups overestimated sleep latency but underestimated wakefulness after sleep onset. The insomnia group underestimated total sleep time by a median of 81 min. However, contrary to our hypothesis, measures of fragmentation (N1, arousal index, sleep efficiency, etc.) did not correlate with the subjective sleep duration estimates. To unmask a potential relationship between sleep architecture and subjective duration, we tested three hypotheses: N1 is perceived as wake; sleep bouts under 10 min are perceived as wake; or N1 and N2 are perceived in a weighted fashion. None of these hypotheses exposed a match between subjective and objective sleep duration. We show only modest performance of a Naïve Bayes Classifier algorithm for predicting mismatch using clinical and polysomnographic variables. Subjective-objective mismatch is common in patients reporting insomnia symptoms. We conclude that mismatch was not attributable to commonly measured polysomnographic measures of fragmentation. Further insight is needed into the complex relationships between subjective perception of sleep and conventional, objective measurements.