Background: Brain-derived neurotrophic factor (BDNF) and nerve growth factor (NGF) are involved in neuroadaptation and foster survival of central and peripheral neurons. In this study, we addressed the question whether BDNF and NGF serum concentrations change during subacute alcohol withdrawal in patients with alcohol dependence compared to healthy controls. Methods: Fifteen patients (age 48.6 ± 7 years) and 15 healthy age-matched controls (age 48.8 ± 7 years) participated consecutively in a 2-week withdrawal study. Results: Mean BDNF levels (7.8 ng/ml, IQR = 4.4–10.7 vs. 16.5 ng/ml, IQR = 13.9–25.6; Z = –3.8, p < 0.0001) and NGF levels (5.8 pg/ml, IQR = 3.8–13.0 vs. 18.4 pg/ml, IQR = 10.9–25.1; Z = –2.5, p = 0.012) were significantly decreased in alcohol-dependent subjects when compared to healthy matched controls. NGF concentrations decreased significantly from day 3 to day 14 (Z = –2.36; p = 0.019). Mean BDNF concentrations showed a tendency to increase after withdrawal from day 3 to day 14 (Z = 1.7; p = 0.078). Conclusion: Decreased NGF and BDNF concentrations in patients suffering from alcohol dependence, which stabilize after physical withdrawal, are in line with withdrawal symptoms and neurological risk factors. In turn, increase of BDNF after acute withdrawal might be connected to neurobiological and behavioral stabilization.