Crohn's disease (CD) may have some severe complications that pose an increasing health burden and negatively impact the quality of life. There are two major types - intestinal and extraintestinal complications, in which immune and non-immune mechanisms take place. We aimed to search for some associations between specific extraintestinal manifestation and intestinal complications in CD patients with some clinicallaboratory findings, immunological markers, and the therapy administered. We examined retrospectively medical files of 26 patients with CD at mean age 42 ± 13 years, including the laboratory results. The immunological markers fecal calprotectin (FC) and fecal lactoferrin (FL) were assessed in frozen fecal samples of the chosen patients. Seventy-three percent of the investigated CD patients had some extraintestinal manifestation and/or intestinal complications, at least 13/26 had intestinal complications. All three patients with extraintestinal signs were positive for FC and 2/3 were positive for FL. We observed a higher serum level of CRP (24.49 mg/l vs. 3.13 mg/l, p = 0.010), slightly lowered serum level of hemoglobin (120 g/l vs. 145 g/l, p = 0.044) and about 2-fold lower iron level (7.23 μmol/l vs. 14.0 μmol/l, p = 0.019) in patients with intestinal complications compared to patients without complications, respectively. Four out of thirteen patients with intestinal complications were without immunosuppressive therapy at the time of our study, and nine out of thirteen - on immunosuppressive drugs. Routine laboratory and immunology testing could be beneficial for gastroenterologists in identifying patients at high risk for the development of complications and in the decision making for more aggressive therapy early after diagnosis.