The aim of our research was to find new biomarkers that could be potentially used in the diagnosis, differentiation and monitoring of inflammatory bowel diseases (IBD). Since extracellular matrix (ECM) remodeling contributes to the pathological changes occurring in IBD, the serum profile of ECM-related proteins may reflect disease activity in the intestinal mucosa. Serum laminin (LM), fibronectin (FN) and gelatinase-associated lipocalin (NGAL) concentrations were determined in 51 patients with IBD before and after a year of treatment, as well as in 48 healthy individuals. A significant difference in serum concentration of FN (130,56 ± 52.87 vs. 287.93 ± 79.69, p < 0.001) and NGAL (133.34 ± 51.51 vs. 102.37.39, p < 0.05) between patients with ulcerative colitis (UC) and healthy individuals was found. In patients with Crohn’s disease (CD), serum concentrations of LM (1329.5 ± 389.36 vs. 1012.07 ± 260.85, p < 0.005) and NGAL (138.94 ± 51.31 vs. 102.65 ± 37.39, p < 0.05) were increased, while FN (89.26 ± 43.86 vs. 287.93 ± 79.69, p < 0.001) was decreased compared to healthy subjects. Moreover, a significant correlation was found between the Mayo score in patients with UC and the levels of NGAL (r = 0.49, p < 0.01) and LM (r = 0.035, p < 0.005), respectively. Another significant correlation was noted between the Crohn’s Disease Activity Index (CDAI) and LM (r = 0.49, p < 0.05) levels in CD group. The results presented in our studies indicate that ECM-related markers might be potential additional tools helpful in diagnosing IBD, differential diagnosis of UC and CD and monitoring the disease activity.