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Parasitic nematodes and their products are promising candidates for therapeutics against inflammatory bowel diseases (IBD). Two species of nematodes, the hookworm <i>Necator americanus</i> and the whipworm <i>Trichuis suis</i>, are being used in clinical treatment trials of IBD referred to as “helminth therapy”. <i>Heligmosomoides polygyrus</i> is a well-known model for human hookworm infections. Excretory–secretory (ES) products of <i>H. polygyrus</i> L4 stage that developed during colitis show a different immunomodulatory effect compared to the ES of <i>H. polgyrus</i> from healthy mice. The aim of the study was to evaluate excretory–secretory proteins produced by <i>H. polygyrus</i> L4 stage males and females that developed in the colitic milieu. Mass spectrometry was used to identify proteins. Blast2GO was used to investigate the functions of the discovered proteins. A total of 387 proteins were identified in the ES of <i>H. polygyrus</i> L4 males (HpC males), and 330 proteins were identified in the ES of L4 females that developed in the colitic milieu (HpC females). In contrast, only 200 proteins were identified in the ES of L4 males (Hp males) and 218 in the ES of L4 females (Hp females) that developed in control conditions. Most of the proteins (123) were detected in all groups. Unique proteins identified in the ES of HpC females included annexin, lysozyme-2, apyrase, and galectin. Venom allergen/Ancylostoma-secreted protein-like, transthyretin-like family proteins, and galectins were found in the secretome of HpC males but not in the secretome of control males. These molecules may be responsible for the therapeutic effects of nematodes in DSS-induced colitis.