Many patients with unilateral renal agenesis have associated abnormalities in other organ systems. Indeed, the absence of a kidney may not even be discovered until an associated abnormality is investigated. Many of these abnormalities occur in structures derived from the mesonephric or paramesonephric ducts, suggesting a defect in the intermediate mesoderm early in development. In males, the ipsilateral mesonephric duct derivatives (vas deferens, seminal gland [vesicle], and epididymis) may be absent or rudimentary (i.e., a seminal gland [vesicle] cyst). Meanwhile, in females, a common associated anomaly is a unicornuate uterus, in which the side ipsilateral to the absent kidney is missing.

Associated abnormalities may also occur in the cardiovascular system (e.g., septal or valvular defects) or gastrointestinal systems (e.g., imperforate anus). Nearby musculoskeletal abnormalities may also be seen. In a smaller subset of patients, unilateral renal agenesis may be associated with a genetic syndrome that affects numerous organ systems, such as BOR (branchio-oto-renal) syndrome, Turner syndrome, Fanconi anemia, Kallmann syndrome, VACTERL (vertebral anomalies, anal atresia, cardiac defects, tracheoesophageal fistula, renal defects, limb defects), and others.