Abstract: Sleep patterns in critically ill patients’ polysomnographic sleep studies (PSG) are severely abnormal. Purpose: We aimed to investigate the association of atypical sleep patterns, micro-sleep phenomena (sleep spindles and K-complexes) and rapid eye movement (REM) sleep with intensive care unit (ICU), in-hospital and 90-day mortality in conscious critically ill patients on mechanical ventilation. Method: This was a prospective descriptive study. We analysed 52 PSGs recorded in conscious critically ill patients on mechanical ventilation. PSGs were scored according to standard classification when possible. Otherwise, modified classification proposed for scoring sleep in critically ill patients was used. The association of PSG findings with mortality was studied using logistic regression and Weibull model of survival analysis. Results: The presence of atypical sleep patterns in accordance with modified sleep scoring classification was associated with higher odds for ICU mortality (odds ratio 11.63; p = 0.03). The absence of K-complexes was associated with higher odds for ICU mortality (odds ratio 11.63; p = 0.03), while the absence of sleep spindles was associated with higher odds for in-hospital (odds ratio 7.80; p = 0.02) and 90-day mortality (odds ratio 5.51; p = 0.02). Loss of sleep spindles was associated with higher mortality risk with cutoff point 90 days (hazard ratio 3.87; p = 0.03). Conclusions: The presence of atypical sleep and absence of normal PSG sleep characteristics in conscious critically ill patients on mechanical ventilation indicates involvement of sleep producing brain structures in the pathological process and is associated with poor outcome.