The SmokeFreeBrain (SFB), which is an EU, H2020-funded project aims to compare several antismoking approaches. Among them, the varenicline intervention seems to be extremely robust in terms of nicotine abstinence rate. However, there are some reports of side effects during sleep associated with insomnia and negatively aroused dreaming. However, these symptoms have never been objectively quantified. This study presents preliminary results from 17 participants who underwent entire polysomnographic (PSG) recordings before and 21 days after the intervention initiation. Our aim was to investigate how both smoking abstinence and varenicline treatment affect sleep quality. We employed both visual sleep scoring and functional connectivity analysis. The purpose of visual sleep scoring analysis, performed according to the guidelines of the American Association of Sleep Medicine (AASM) was to investigate sleep macro-architecture, defined as the sleep cycles during night. We calculated various sleep parameters like efficiency, onset, stage and latency duration, sleep fragmentation and the number of arousals during sleep. Additionally, we also estimated the co-operative degree among electroencephalographic time series as well as the interactions among brain and heart. The latter analysis aimed to quantify neuroplasticity changes associated both with smoking cessation and varenicline treatment. Early results demonstrated beneficial effects from nicotine abstinence (increased oxygen saturation level, facilitated sleep onset). However, there were neurophysiological patterns of increased arousal both on autonomic (heart rate variability features) and on cortical level (increased connectivity within beta band). These patterns observed even during deep sleep stages indicating poor sleep quality.