We aimed to study complex cardiovagal control using heart rate variability (HRV), linear and nonlinear analyses at rest and during negative emotional stress in healthy students with varying depressive symptoms. ECG recording in 20 students was performed at baseline, negative emotional stress, and recovery period. The HRV parameters evaluated were the following: RR interval, spectral power in high-frequency band (HF-HRV), and symbolic dynamics index 2LV%. The subjects were divided into two groups based on the score of the Beck Depression Inventory (BDI) - normal mood (BDI: 0.6 +/- 0.2) and mild mood disturbance (BDI: 14.3 +/- 1.4). We found significantly lower logHF-HRV during emotional stress in mild mood disturbance compared with normal mood (p = 0.047). No significant differences were found in the remaining parameters. We conclude that negative emotional stress attenuated the cardiovagal control during mood disturbance, which points to discrete abnormalities in the neurocardiac reflex system associated with depressive symptoms. Hampered cardiovagal control could represent a potential pathomechanism leading to depression-linked cardiovascular complications.