Lymphocytic colitis which is more common in women than in men has been associated with autoimmune conditions, and hormones are thought to play a role. The effect of pregnancy on the clinical course of women with lymphocytic colitis has not yet been reported. We describe a case of chronic watery diarrhea in a woman with psoriasis and lymphocytic colitis that has relapsed after successful treatment with budesonide had been stopped before undergoing modern assisted reproductive care. Elevated stool frequencies diminished after in vitro fertilization and remained normal throughout pregnancy when no systemic immunosuppressive therapy was administered and plaque psoriasis slightly worsened under local symptomatic treatment. After preterm birth and early breastfeeding cessation, chronic watery diarrhea, however, recurred. This clinical observation suggests that pregnancy influences the overall course of chronic watery diarrhea of autoimmune-associated microscopic colitis.