Heart rate variability (HRV) is a noninvasive technique to detect changes in the autonomous nervous system. It has rarely been investigated in horses with colic. Therefore, the objective was to assess the evolution of HRV parameters and cortisol concentrations in horses with colic. The 43 horses included in this study were categorized into three groups according to the treatment (1, surgical; 2, conservative; 3, euthanized). The HRV and laboratory variables were measured at admission (T1), the day after admission (T2), and at discharge (T3) and compared between groups and over time with an ANOVA with Bonferroni correction. Relationships between the HRV parameters themselves and the laboratory variables was assessed by Pearson correlation coefficients. Evolution of the heart rate (HR) over time, mean normal to normal R intervals (meanNN) and cortisol concentrations indicate a decreased sympathetic stimulation over time in group 1 and 2, in contrast to group 3. For group 3, the meanNN and HR differed significantly to group 2 at T1 and to group 1 and 2 at T2. Treatment induced a change in the HRV and cortisol response in horses managed conservatively or surgically but not in horses that required euthanasia. However, further studies are required to assess the validity of HRV analyses in horses with colic.