Probiotics have gained increasing clinical attention as adjunctive treatment for lower gastrointestinal disorders. However, evidence supporting their therapeutic efficacy remains limited, particularly with regard to sex-related differences. This expert review provides evidence-based insights and practical recommendations for the use of probiotics in patients with irritable bowel syndrome (IBS), functional constipation (FC), and Clostridioides difficile infection (CDI), considering possible sex-related differences. Evidence from randomized controlled trials and meta-analyses indicates that probiotics can modestly improve global symptoms, abdominal pain, and bloating in IBS and enhance bowel movement frequency and stool consistency in FC. However, these effects are strain-specific and heterogeneous. Although clinical studies on probiotics in IBS have not confirmed significant sex-related differences, experimental animal studies using stress-induced IBS models have demonstrated sex-dependent responses to specific probiotic strains, supporting the biological plausibility of such differences. For CDI, the efficacy of probiotics in preventing primary or recurrent infections remains inconsistent across large trials, and current guidelines usually do not recommend their routine use. However, sex and age difference of immunology supports the clinical differences of CDI. Probiotics are generally considered safe for healthy individuals, although caution is advised in patients who are immunocompromised or critically ill. Clinicians should select probiotic products based on strain-specific clinical evidence, adequate viable doses, patient's characteristics, or patient's sex. In conclusion, probiotics might play a role as adjunctive therapy for IBS and FC, with variability in responses influenced by microbial, host, and potential sex-related factors. Further research is needed to establish optimized personalized probiotic strategies.