In the etiology of discogenic pain, attention is paid to the role of neurotrophic factors, which include classic neurotrophins (NTs). This study aimed to assess changes in the concentrations of NT-3 and NT-4 in the intervertebral discs (IVDs) of the lumbosacral (L/S) spine depending on the advancement of degenerative changes, pain severity, habits, and comorbidities. The study group included 113 patients who underwent microdiscectomy due to degenerative IVD disease of the L/S spine. The severity of degenerative IVD changes was assessed using the five-point Pfirrmann scale, and the pain intensity was assessed according to the visual analog scale (VAS). In turn, the control group included 81 participants from whom IVDs of the L/S section of the spine were collected post-mortem during forensic autopsy or organ donation. At the mRNA level, we noted NT-3 overexpression in the test samples compared with the controls (fold change (FC) = 9.12 ± 0.56; p < 0.05), while NT-4 transcriptional activity was decreased in the test samples compared with the controls (FC = 0.33 ± 0.07; p < 0.05). However, at the protein level, the concentrations of NT-3 (134 ± 5.78 pg/mL vs. 6.78 ± 1.17 pg/mL; p < 0.05) and NT-4 (316.77 ± 8.19 pg/mL vs. 76.92 ± 4.82 pg/mL; p < 0.05) were significantly higher in the test samples compared with the control samples. Nevertheless, the concentration of both proteins did not statistically significantly change depending on the advancement of degenerative changes and the pain intensity (p > 0.05). In addition, higher levels of NT-3 and NT-4 were noted in IVD samples from patients who consumed alcohol, smoked tobacco, were overweight/obese, or had comorbid diabetes compared with patients without these risk factors (p < 0.05). Our analysis confirmed that differences in the degenerative process of IVD, energy metabolism, and lifestyle are related to changes in the concentration profiles of NT-3 and NT-4.